From 19132fff4a12861e0c68b6aa959613329dafd271 Mon Sep 17 00:00:00 2001
From: gennadyFauna <153561808+gennadyFauna@users.noreply.github.com>
Date: Mon, 22 Jan 2024 13:37:45 -0800
Subject: [PATCH 01/34] first commit: bump up kb versions

---
 modules/nf-core/kallistobustools/count/environment.yml | 2 +-
 modules/nf-core/kallistobustools/count/main.nf         | 4 ++--
 modules/nf-core/kallistobustools/ref/environment.yml   | 2 +-
 modules/nf-core/kallistobustools/ref/main.nf           | 4 ++--
 4 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/modules/nf-core/kallistobustools/count/environment.yml b/modules/nf-core/kallistobustools/count/environment.yml
index 7ff8a2da..024f0afc 100644
--- a/modules/nf-core/kallistobustools/count/environment.yml
+++ b/modules/nf-core/kallistobustools/count/environment.yml
@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::kb-python=0.27.2
+  - bioconda::kb-python=0.28.2
diff --git a/modules/nf-core/kallistobustools/count/main.nf b/modules/nf-core/kallistobustools/count/main.nf
index 036bb35d..bfd9a625 100644
--- a/modules/nf-core/kallistobustools/count/main.nf
+++ b/modules/nf-core/kallistobustools/count/main.nf
@@ -4,8 +4,8 @@ process KALLISTOBUSTOOLS_COUNT {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/kb-python:0.27.2--pyhdfd78af_0' :
-        'biocontainers/kb-python:0.27.2--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/kb-python:0.28.2--pyhdfd78af_0' :
+        'biocontainers/kb-python:0.28.2--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(reads)
diff --git a/modules/nf-core/kallistobustools/ref/environment.yml b/modules/nf-core/kallistobustools/ref/environment.yml
index acbd0e0a..6ae07a8c 100644
--- a/modules/nf-core/kallistobustools/ref/environment.yml
+++ b/modules/nf-core/kallistobustools/ref/environment.yml
@@ -4,5 +4,5 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::kb-python=0.27.2
+  - bioconda::kb-python=0.28.2
   - conda-forge::requests>=2.23.0
diff --git a/modules/nf-core/kallistobustools/ref/main.nf b/modules/nf-core/kallistobustools/ref/main.nf
index 68d72ca9..759e8663 100644
--- a/modules/nf-core/kallistobustools/ref/main.nf
+++ b/modules/nf-core/kallistobustools/ref/main.nf
@@ -4,8 +4,8 @@ process KALLISTOBUSTOOLS_REF {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/kb-python:0.27.2--pyhdfd78af_0' :
-        'biocontainers/kb-python:0.27.2--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/kb-python:0.28.2--pyhdfd78af_0' :
+        'biocontainers/kb-python:0.28.2--pyhdfd78af_0' }"
 
     input:
     path fasta

From 4ef499e6d856b76e7a6010f3c0e10abb63edf940 Mon Sep 17 00:00:00 2001
From: gennadyFauna <153561808+gennadyFauna@users.noreply.github.com>
Date: Mon, 29 Jan 2024 14:47:27 -0800
Subject: [PATCH 02/34] renaming parameters

---
 .../nf-core/kallistobustools/count/main.nf    |  4 ++--
 .../nf-core/kallistobustools/count/meta.yml   | 10 ++++-----
 .../kallistobustools/ref/environment.yml      |  2 +-
 modules/nf-core/kallistobustools/ref/main.nf  |  8 +++----
 modules/nf-core/kallistobustools/ref/meta.yml | 22 +++++++++----------
 5 files changed, 23 insertions(+), 23 deletions(-)

diff --git a/modules/nf-core/kallistobustools/count/main.nf b/modules/nf-core/kallistobustools/count/main.nf
index bfd9a625..df81a097 100644
--- a/modules/nf-core/kallistobustools/count/main.nf
+++ b/modules/nf-core/kallistobustools/count/main.nf
@@ -27,7 +27,7 @@ process KALLISTOBUSTOOLS_COUNT {
     def args    = task.ext.args ?: ''
     def prefix  = task.ext.prefix ?: "${meta.id}"
     def cdna    = t1c ? "-c1 $t1c" : ''
-    def introns = t2c ? "-c2 $t2c" : ''
+    def unprocessed = t2c ? "-c2 $t2c" : ''
     def memory  = task.memory.toGiga() - 1
     """
     kb \\
@@ -36,7 +36,7 @@ process KALLISTOBUSTOOLS_COUNT {
         -i $index \\
         -g $t2g \\
         $cdna \\
-        $introns \\
+        $unprocessed \\
         -x $technology \\
         $args \\
         -o ${prefix}.count \\
diff --git a/modules/nf-core/kallistobustools/count/meta.yml b/modules/nf-core/kallistobustools/count/meta.yml
index 7491248c..c8763343 100644
--- a/modules/nf-core/kallistobustools/count/meta.yml
+++ b/modules/nf-core/kallistobustools/count/meta.yml
@@ -34,16 +34,16 @@ input:
       pattern: "*t2g.txt"
   - t1c:
       type: file
-      description: kb ref's c1 spliced_t2c file
+      description: kb ref's c1 cdna_t2c file
       pattern: "*.{cdna_t2c.txt}"
   - t2c:
       type: file
-      description: kb ref's c2 unspliced_t2c file
-      pattern: "*.{introns_t2c.txt}"
+      description: kb ref's c2 unprocessed_t2c file
+      pattern: "*.{unprocessed_t2c.txt}"
   - workflow_mode:
       type: string
-      description: String value defining workflow to use, can be one of "standard", "lamanno", "nucleus"
-      pattern: "{standard,lamanno,nucleus,kite}"
+      description: String value defining workflow to use, can be one of "standard", "nac", "lamanno" (obsolete)
+      pattern: "{standard,lamanno,nac}"
   - technology:
       type: string
       description: String value defining the sequencing technology used.
diff --git a/modules/nf-core/kallistobustools/ref/environment.yml b/modules/nf-core/kallistobustools/ref/environment.yml
index 6ae07a8c..62942e01 100644
--- a/modules/nf-core/kallistobustools/ref/environment.yml
+++ b/modules/nf-core/kallistobustools/ref/environment.yml
@@ -5,4 +5,4 @@ channels:
   - defaults
 dependencies:
   - bioconda::kb-python=0.28.2
-  - conda-forge::requests>=2.23.0
+  - conda-forge::requests>=2.23.0
\ No newline at end of file
diff --git a/modules/nf-core/kallistobustools/ref/main.nf b/modules/nf-core/kallistobustools/ref/main.nf
index 759e8663..989f86f3 100644
--- a/modules/nf-core/kallistobustools/ref/main.nf
+++ b/modules/nf-core/kallistobustools/ref/main.nf
@@ -17,9 +17,9 @@ process KALLISTOBUSTOOLS_REF {
     path "kb_ref_out.idx" , emit: index
     path "t2g.txt"        , emit: t2g
     path "cdna.fa"        , emit: cdna
-    path "intron.fa"      , optional:true, emit: intron
+    path "unprocessed.fa"      , optional:true, emit: unprocessed
     path "cdna_t2c.txt"   , optional:true, emit: cdna_t2c
-    path "intron_t2c.txt" , optional:true, emit: intron_t2c
+    path "unprocessed_t2c.txt" , optional:true, emit: unprocessed_t2c
 
     when:
     task.ext.when == null || task.ext.when
@@ -49,9 +49,9 @@ process KALLISTOBUSTOOLS_REF {
             -i kb_ref_out.idx \\
             -g t2g.txt \\
             -f1 cdna.fa \\
-            -f2 intron.fa \\
+            -f2 unprocessed.fa \\
             -c1 cdna_t2c.txt \\
-            -c2 intron_t2c.txt \\
+            -c2 unprocessed_t2c.txt \\
             --workflow $workflow_mode \\
             $fasta \\
             $gtf
diff --git a/modules/nf-core/kallistobustools/ref/meta.yml b/modules/nf-core/kallistobustools/ref/meta.yml
index 00be5143..1ca31c57 100644
--- a/modules/nf-core/kallistobustools/ref/meta.yml
+++ b/modules/nf-core/kallistobustools/ref/meta.yml
@@ -26,8 +26,8 @@ input:
       pattern: "*.{gtf,gtf.gz}"
   - workflow_mode:
       type: string
-      description: String value defining workflow to use, can be one of "standard", "lamanno", "nucleus"
-      pattern: "{standard,lamanno,nucleus}"
+      description: String value defining workflow to use, can be one of "standard", "nac", "lamanno" (obsolete)
+      pattern: "{standard,lamanno,nac}"
 output:
   - versions:
       type: file
@@ -43,21 +43,21 @@ output:
       pattern: "*t2g.{txt}"
   - cdna:
       type: file
-      description: Cdna fasta file
+      description: cDNA fasta file
       pattern: "*cdna.{fa}"
-  - intron:
+  - unprocessed:
       type: file
-      description: intron fasta file
-      pattern: "*intron.{fa}"
+      description: Unprocessed fasta file
+      pattern: "*unprocessed.{fa}"
   - cdna_t2c:
       type: file
-      description: cdna transcript to capture file
+      description: cDNA transcript to capture file
       pattern: "*cdna_t2c.{txt}"
-  - intron_t2c:
+  - unprocessed_t2c:
       type: file
-      description: intron transcript to capture file
-      pattern: "*intron_t2c.{txt}"
+      description: Unprocessed transcript to capture file
+      pattern: "*unprocessed_t2c.{txt}"
 authors:
-  - "@flowuenne"
+  - "@flowuenne" 
 maintainers:
   - "@flowuenne"

From fb6db73e2c2a928222e79ebad7ba61f2f0f239b1 Mon Sep 17 00:00:00 2001
From: gennadyFauna <153561808+gennadyFauna@users.noreply.github.com>
Date: Mon, 29 Jan 2024 14:56:45 -0800
Subject: [PATCH 03/34] Memory arg might need to be before fastq list?

---
 modules/nf-core/kallistobustools/count/main.nf | 4 ++--
 subworkflows/local/kallisto_bustools.nf        | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/modules/nf-core/kallistobustools/count/main.nf b/modules/nf-core/kallistobustools/count/main.nf
index df81a097..fac39a91 100644
--- a/modules/nf-core/kallistobustools/count/main.nf
+++ b/modules/nf-core/kallistobustools/count/main.nf
@@ -40,8 +40,8 @@ process KALLISTOBUSTOOLS_COUNT {
         -x $technology \\
         $args \\
         -o ${prefix}.count \\
-        ${reads.join( " " )} \\
-        -m ${memory}G
+        -m ${memory}G \\
+        ${reads.join( " " )} 
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/subworkflows/local/kallisto_bustools.nf b/subworkflows/local/kallisto_bustools.nf
index 3210e47a..41387683 100644
--- a/subworkflows/local/kallisto_bustools.nf
+++ b/subworkflows/local/kallisto_bustools.nf
@@ -46,7 +46,7 @@ workflow KALLISTO_BUSTOOLS {
         kallisto_index = KALLISTOBUSTOOLS_REF.out.index.collect()
         ch_versions = ch_versions.mix(KALLISTOBUSTOOLS_REF.out.versions)
         t1c = KALLISTOBUSTOOLS_REF.out.cdna_t2c.ifEmpty{ [] }
-        t2c = KALLISTOBUSTOOLS_REF.out.intron_t2c.ifEmpty{ [] }
+        t2c = KALLISTOBUSTOOLS_REF.out.unprocessed_t2c.ifEmpty{ [] }
     }
 
     /*

From 3ccd0833c6509aab95beeae252ae702ad1b7d955 Mon Sep 17 00:00:00 2001
From: gennadyFauna <153561808+gennadyFauna@users.noreply.github.com>
Date: Mon, 29 Jan 2024 15:35:06 -0800
Subject: [PATCH 04/34] Update main.nf

---
 modules/nf-core/kallistobustools/count/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/kallistobustools/count/main.nf b/modules/nf-core/kallistobustools/count/main.nf
index fac39a91..9e860241 100644
--- a/modules/nf-core/kallistobustools/count/main.nf
+++ b/modules/nf-core/kallistobustools/count/main.nf
@@ -41,7 +41,7 @@ process KALLISTOBUSTOOLS_COUNT {
         $args \\
         -o ${prefix}.count \\
         -m ${memory}G \\
-        ${reads.join( " " )} 
+        ${reads.join( " " )}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

From 45e0b1963f36164f6dbf6db672825b8b7b52724a Mon Sep 17 00:00:00 2001
From: gennadyFauna <153561808+gennadyFauna@users.noreply.github.com>
Date: Fri, 9 Feb 2024 16:55:00 -0800
Subject: [PATCH 05/34] Removed t2g versions call
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

That is not really what this argument does – it just concatenates the gene_version and transcript_version fields to IDs.
---
 subworkflows/local/kallisto_bustools.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/subworkflows/local/kallisto_bustools.nf b/subworkflows/local/kallisto_bustools.nf
index 41387683..8de01794 100644
--- a/subworkflows/local/kallisto_bustools.nf
+++ b/subworkflows/local/kallisto_bustools.nf
@@ -34,7 +34,7 @@ workflow KALLISTO_BUSTOOLS {
     if (!txp2gene && kallisto_index) {
         GENE_MAP( gtf )
         txp2gene = GENE_MAP.out.gene_map
-        ch_versions = ch_versions.mix(GENE_MAP.out.versions)
+        /* --    ch_versions = ch_versions.mix(GENE_MAP.out.versions)    -- */
     }
 
     /*

From 50d3948ba65aa88644fa18bc8ee6240fe6760ce4 Mon Sep 17 00:00:00 2001
From: gennadyFauna <153561808+gennadyFauna@users.noreply.github.com>
Date: Mon, 12 Feb 2024 11:18:22 -0800
Subject: [PATCH 06/34] removing t2g.py

The txp2gene file should really be generated by kallisto|bustools. The t2g.py script generates a 3-column rather than 7-column t2g, which seems to be incompatible with kb count.
---
 modules/local/gene_map.nf               | 34 -------------------------
 subworkflows/local/kallisto_bustools.nf | 20 +++------------
 2 files changed, 3 insertions(+), 51 deletions(-)
 delete mode 100644 modules/local/gene_map.nf

diff --git a/modules/local/gene_map.nf b/modules/local/gene_map.nf
deleted file mode 100644
index 9fd29e0a..00000000
--- a/modules/local/gene_map.nf
+++ /dev/null
@@ -1,34 +0,0 @@
-/*
- * Reformat design file and check validity
- */
-process GENE_MAP {
-    tag "$gtf"
-    label 'process_low'
-
-    conda "conda-forge::python=3.8.3"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/python:3.8.3' :
-        'biocontainers/python:3.8.3' }"
-
-    input:
-    path gtf
-
-    output:
-    path "transcripts_to_genes.txt" , emit: gene_map
-
-    when:
-    task.ext.when == null || task.ext.when
-
-    script:
-    if("${gtf}".endsWith('.gz')){
-        name = "${gtf.baseName}"
-        unzip = "gunzip -f ${gtf}"
-    } else {
-        unzip = ""
-        name = "${gtf}"
-    }
-    """
-    $unzip
-    cat $name | t2g.py --use_version > transcripts_to_genes.txt
-    """
-}
diff --git a/subworkflows/local/kallisto_bustools.nf b/subworkflows/local/kallisto_bustools.nf
index 8de01794..7edd98d5 100644
--- a/subworkflows/local/kallisto_bustools.nf
+++ b/subworkflows/local/kallisto_bustools.nf
@@ -1,5 +1,4 @@
 /* --    IMPORT LOCAL MODULES/SUBWORKFLOWS     -- */
-include { GENE_MAP }                          from '../../modules/local/gene_map'
 include {KALLISTOBUSTOOLS_COUNT }             from '../../modules/nf-core/kallistobustools/count/main'
 
 /* --    IMPORT NF-CORE MODULES/SUBWORKFLOWS   -- */
@@ -21,26 +20,13 @@ workflow KALLISTO_BUSTOOLS {
     main:
     ch_versions = Channel.empty()
 
-    assert kallisto_index || (genome_fasta && gtf):
+    assert (txp2gene && kallisto_index) || (genome_fasta && gtf):
         "Must provide a genome fasta file ('--fasta') and a gtf file ('--gtf') if no index is given!"
 
-    assert txp2gene || gtf:
-        "Must provide either a GTF file ('--gtf') or kallisto gene map ('--kallisto_gene_map') to align with kallisto bustools!"
-
-    /*
-    * Generate Kallisto Gene Map if not supplied and index is given
-    * If no index is given, the gene map will be generated in the 'kb ref' step
-    */
-    if (!txp2gene && kallisto_index) {
-        GENE_MAP( gtf )
-        txp2gene = GENE_MAP.out.gene_map
-        /* --    ch_versions = ch_versions.mix(GENE_MAP.out.versions)    -- */
-    }
-
     /*
-    * Generate kallisto index
+    * Generate kallisto index and t2g if not already present
     */
-    if (!kallisto_index) {
+    if (!(txp2gene && kallisto_index)) {
         KALLISTOBUSTOOLS_REF( genome_fasta, gtf, kb_workflow )
         txp2gene = KALLISTOBUSTOOLS_REF.out.t2g.collect()
         kallisto_index = KALLISTOBUSTOOLS_REF.out.index.collect()

From b0d7c5d0dcd523d0c0c143d6a00a7f4c16bcbdd3 Mon Sep 17 00:00:00 2001
From: gennadyFauna <153561808+gennadyFauna@users.noreply.github.com>
Date: Mon, 12 Feb 2024 11:20:40 -0800
Subject: [PATCH 07/34] Remove txp2gene.collect() call

This .collect() is incompatible with passing in an existing t2g, and superfluous given the .collect() after the kb ref call.
---
 subworkflows/local/kallisto_bustools.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/subworkflows/local/kallisto_bustools.nf b/subworkflows/local/kallisto_bustools.nf
index 7edd98d5..5b3283a4 100644
--- a/subworkflows/local/kallisto_bustools.nf
+++ b/subworkflows/local/kallisto_bustools.nf
@@ -52,7 +52,7 @@ workflow KALLISTO_BUSTOOLS {
     emit:
     ch_versions
     counts = KALLISTOBUSTOOLS_COUNT.out.count
-    txp2gene = txp2gene.collect()
+    txp2gene
 
 
 }

From 8630ef926817af9fc071143d2e476888305e9f04 Mon Sep 17 00:00:00 2001
From: gennadyFauna <153561808+gennadyFauna@users.noreply.github.com>
Date: Mon, 12 Feb 2024 13:21:15 -0800
Subject: [PATCH 08/34] add t1c/t2c parameters to schema

t1c and t2c are required to run nac and lamanno count workflows. Since they are already defined when running kb ref, they cannot be easily defined through ext.args when using an existing reference
---
 nextflow.config                         |  4 +++-
 nextflow_schema.json                    | 10 ++++++++++
 subworkflows/local/kallisto_bustools.nf |  2 ++
 3 files changed, 15 insertions(+), 1 deletion(-)

diff --git a/nextflow.config b/nextflow.config
index 9e83c42a..9c3ac851 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -26,10 +26,12 @@ params {
     txp2gene          = null
     salmon_index      = null
 
-    // kallist bustools parameters
+    // kallisto bustools parameters
     kallisto_gene_map = null
     kallisto_index    = null
     kb_workflow       = "standard"
+    kb_t1c            = null
+    kb_t2c            = null
 
     // STARsolo parameters
     star_index          = null
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 34af4c64..e9ca04d9 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -213,6 +213,16 @@
                     "description": "Specify a path to the precomputed Kallisto index.",
                     "fa_icon": "fas fa-fish"
                 },
+                "kb_t1c": {
+                    "type": "string",
+                    "description": "Specify a path to the cDNA transcripts-to-capture.",
+                    "fa_icon": "fas fa-fish"
+                },
+                "kb_t2c": {
+                    "type": "string",
+                    "description": "Specify a path to the intron transcripts-to-capture.",
+                    "fa_icon": "fas fa-fish"
+                },
                 "kb_workflow": {
                     "type": "string",
                     "default": "standard",
diff --git a/subworkflows/local/kallisto_bustools.nf b/subworkflows/local/kallisto_bustools.nf
index 5b3283a4..7fdaf8ef 100644
--- a/subworkflows/local/kallisto_bustools.nf
+++ b/subworkflows/local/kallisto_bustools.nf
@@ -13,6 +13,8 @@ workflow KALLISTO_BUSTOOLS {
     gtf
     kallisto_index
     txp2gene
+    t1c
+    t2c
     protocol
     kb_workflow
     ch_fastq

From e503e218326fa852fb95ac2d77d88e20fec1d1d9 Mon Sep 17 00:00:00 2001
From: gennadyFauna <153561808+gennadyFauna@users.noreply.github.com>
Date: Mon, 12 Feb 2024 13:29:55 -0800
Subject: [PATCH 09/34] Fixed kallisto_gene_map documentation

scrnaseq does not actually use kallisto_gene_map anywhere.
Changed kallisto icon from a salmon to a rainbow (there is no bear icon, but bustools uses the Pink Floyd-esque prism image, so it seems most appropriate)
---
 nextflow_schema.json | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/nextflow_schema.json b/nextflow_schema.json
index e9ca04d9..b94b6460 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -155,7 +155,7 @@
                 "txp2gene": {
                     "type": "string",
                     "description": "Path to transcript to gene mapping file. This allows the specification of a transcript to gene mapping file for Salmon Alevin and AlevinQC.",
-                    "help_text": "> This is not the same as the `kallisto_gene_map` parameter down below and is only used by the Salmon Alevin workflow.",
+                    "help_text": "> This is the same as the `kallisto_gene_map` parameter below.",
                     "fa_icon": "fas fa-map-marked-alt"
                 },
                 "simpleaf_rlen": {
@@ -203,31 +203,31 @@
             "default": "",
             "fa_icon": "fas fa-fish",
             "properties": {
-                "kallisto_gene_map": {
-                    "type": "string",
-                    "description": "Specify a Kallisto gene mapping file here. If you don't, this will be automatically created in the Kallisto workflow when specifying a valid `--gtf` file.",
-                    "fa_icon": "fas fa-fish"
-                },
                 "kallisto_index": {
                     "type": "string",
                     "description": "Specify a path to the precomputed Kallisto index.",
-                    "fa_icon": "fas fa-fish"
+                    "fa_icon": "fas fa-rainbow"
+                },
+                "txp2gene": {
+                    "type": "string",
+                    "description": "Specify a Kallisto gene mapping file here. If you don't, this will be automatically created in the Kallisto workflow when specifying a valid `--gtf` file.",
+                    "fa_icon": "fas fa-rainbow"
                 },
                 "kb_t1c": {
                     "type": "string",
                     "description": "Specify a path to the cDNA transcripts-to-capture.",
-                    "fa_icon": "fas fa-fish"
+                    "fa_icon": "fas fa-rainbow"
                 },
                 "kb_t2c": {
                     "type": "string",
                     "description": "Specify a path to the intron transcripts-to-capture.",
-                    "fa_icon": "fas fa-fish"
+                    "fa_icon": "fas fa-rainbow"
                 },
                 "kb_workflow": {
                     "type": "string",
                     "default": "standard",
                     "description": "Type of workflow. Use `lamanno` for RNA velocity based on La Manno et al. 2018 logic. Use `nucleus` for RNA velocity on single-nucleus RNA-seq reads. Use `kite` for feature barcoding. Use `kite: 10xFB` for 10x Genomics Feature Barcoding technology. (default: standard)",
-                    "fa_icon": "fas fa-fish",
+                    "fa_icon": "fas fa-rainbow",
                     "enum": ["standard", "lamanno", "nucleus", "kite", "kite: 10xFB"]
                 }
             }

From 752d051df605dbe192339e9446162882b4657d69 Mon Sep 17 00:00:00 2001
From: gennadyFauna <153561808+gennadyFauna@users.noreply.github.com>
Date: Mon, 12 Feb 2024 13:31:59 -0800
Subject: [PATCH 10/34] Update nextflow_schema.json

---
 nextflow_schema.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nextflow_schema.json b/nextflow_schema.json
index b94b6460..56785f0e 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -201,7 +201,7 @@
             "type": "object",
             "description": "Params related to Kallisto/BUS tool",
             "default": "",
-            "fa_icon": "fas fa-fish",
+            "fa_icon": "fas fa-rainbow",
             "properties": {
                 "kallisto_index": {
                     "type": "string",

From 4d90d609f1ececc9421619c572b8aa8a717ab37f Mon Sep 17 00:00:00 2001
From: gennadyFauna <153561808+gennadyFauna@users.noreply.github.com>
Date: Tue, 13 Feb 2024 10:03:11 -0800
Subject: [PATCH 11/34] de-duplicating txp2gene args (lint complains)

---
 nextflow_schema.json | 18 ++++++------------
 1 file changed, 6 insertions(+), 12 deletions(-)

diff --git a/nextflow_schema.json b/nextflow_schema.json
index 56785f0e..0dc716b1 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -138,7 +138,12 @@
                     "default": "s3://ngi-igenomes/igenomes",
                     "fa_icon": "fas fa-cloud-download-alt",
                     "hidden": true
-                }
+                },
+                "txp2gene": {
+                    "type": "string",
+                    "description": "Kallisto or Alevin gene mapping file.",
+                    "fa_icon": "fas map-marked-alt"
+                },
             }
         },
         "alevin_options": {
@@ -152,12 +157,6 @@
                     "description": "This can be used to specify a precomputed Salmon index in the pipeline, in order to skip the generation of required indices by Salmon itself.",
                     "fa_icon": "fas fa-fish"
                 },
-                "txp2gene": {
-                    "type": "string",
-                    "description": "Path to transcript to gene mapping file. This allows the specification of a transcript to gene mapping file for Salmon Alevin and AlevinQC.",
-                    "help_text": "> This is the same as the `kallisto_gene_map` parameter below.",
-                    "fa_icon": "fas fa-map-marked-alt"
-                },
                 "simpleaf_rlen": {
                     "type": "integer",
                     "default": 91,
@@ -208,11 +207,6 @@
                     "description": "Specify a path to the precomputed Kallisto index.",
                     "fa_icon": "fas fa-rainbow"
                 },
-                "txp2gene": {
-                    "type": "string",
-                    "description": "Specify a Kallisto gene mapping file here. If you don't, this will be automatically created in the Kallisto workflow when specifying a valid `--gtf` file.",
-                    "fa_icon": "fas fa-rainbow"
-                },
                 "kb_t1c": {
                     "type": "string",
                     "description": "Specify a path to the cDNA transcripts-to-capture.",

From efb1487d0a6bf6037c789121eeacf63173ba680c Mon Sep 17 00:00:00 2001
From: gennadyFauna <153561808+gennadyFauna@users.noreply.github.com>
Date: Tue, 13 Feb 2024 10:05:39 -0800
Subject: [PATCH 12/34] Update nextflow_schema.json

---
 nextflow_schema.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nextflow_schema.json b/nextflow_schema.json
index 0dc716b1..837ba7a0 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -143,7 +143,7 @@
                     "type": "string",
                     "description": "Kallisto or Alevin gene mapping file.",
                     "fa_icon": "fas map-marked-alt"
-                },
+                }
             }
         },
         "alevin_options": {

From 5ffdc888b8f31e53e7aae1f4d633bb70634a6785 Mon Sep 17 00:00:00 2001
From: gennadyFauna <153561808+gennadyFauna@users.noreply.github.com>
Date: Tue, 13 Feb 2024 10:22:45 -0800
Subject: [PATCH 13/34] txp2gene has to be moved if it's shared

---
 nextflow.config | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/nextflow.config b/nextflow.config
index 9c3ac851..a774d835 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -19,15 +19,14 @@ params {
     // reference files
     genome            = null
     transcript_fasta  = null
+    txp2gene          = null
 
     // salmon alevin parameters (simpleaf)
     simpleaf_rlen     = 91
     barcode_whitelist = null
-    txp2gene          = null
     salmon_index      = null
 
     // kallisto bustools parameters
-    kallisto_gene_map = null
     kallisto_index    = null
     kb_workflow       = "standard"
     kb_t1c            = null

From 38344a5018c0eaffdd6d7552dcb44b98d5133227 Mon Sep 17 00:00:00 2001
From: gennadyFauna <153561808+gennadyFauna@users.noreply.github.com>
Date: Tue, 13 Feb 2024 10:44:28 -0800
Subject: [PATCH 14/34] adding explicit t1c and t2c arguments for kb

Maybe it is possible to somehow inject them with ext.args, but this is a fairly standard pipeline option, and should probably be exposed.
---
 workflows/scrnaseq.nf | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/workflows/scrnaseq.nf b/workflows/scrnaseq.nf
index 25740a8e..63381a6f 100644
--- a/workflows/scrnaseq.nf
+++ b/workflows/scrnaseq.nf
@@ -98,6 +98,8 @@ if (params.barcode_whitelist) {
 //kallisto params
 ch_kallisto_index = params.kallisto_index ? file(params.kallisto_index) : []
 kb_workflow = params.kb_workflow
+kb_t1c = params.kb_t1c ? file(params.kb_t1c) : []
+kb_t2c = params.kb_t2c ? file(params.kb_t2c) : []
 
 //salmon params
 ch_salmon_index = params.salmon_index ? file(params.salmon_index) : []
@@ -144,6 +146,8 @@ workflow SCRNASEQ {
             ch_filter_gtf,
             ch_kallisto_index,
             ch_txp2gene,
+            kb_t1c,
+            kb_t2c,
             protocol_config['protocol'],
             kb_workflow,
             ch_fastq

From bf276856b4159b0da100f33f1c1cb5f8a792e0a6 Mon Sep 17 00:00:00 2001
From: gennadyFauna <153561808+gennadyFauna@users.noreply.github.com>
Date: Fri, 23 Feb 2024 11:32:52 -0800
Subject: [PATCH 15/34] harmonizing with PR while that's in progress

---
 modules/nf-core/kallistobustools/count/main.nf     |  4 ++--
 modules/nf-core/kallistobustools/count/meta.yml    |  4 ++--
 .../nf-core/kallistobustools/ref/environment.yml   |  3 ++-
 modules/nf-core/kallistobustools/ref/main.nf       |  8 ++++----
 modules/nf-core/kallistobustools/ref/meta.yml      | 14 +++++++-------
 5 files changed, 17 insertions(+), 16 deletions(-)

diff --git a/modules/nf-core/kallistobustools/count/main.nf b/modules/nf-core/kallistobustools/count/main.nf
index 9e860241..ce5b5365 100644
--- a/modules/nf-core/kallistobustools/count/main.nf
+++ b/modules/nf-core/kallistobustools/count/main.nf
@@ -27,7 +27,7 @@ process KALLISTOBUSTOOLS_COUNT {
     def args    = task.ext.args ?: ''
     def prefix  = task.ext.prefix ?: "${meta.id}"
     def cdna    = t1c ? "-c1 $t1c" : ''
-    def unprocessed = t2c ? "-c2 $t2c" : ''
+    def intron  = t2c ? "-c2 $t2c" : ''
     def memory  = task.memory.toGiga() - 1
     """
     kb \\
@@ -36,7 +36,7 @@ process KALLISTOBUSTOOLS_COUNT {
         -i $index \\
         -g $t2g \\
         $cdna \\
-        $unprocessed \\
+        $intron \\
         -x $technology \\
         $args \\
         -o ${prefix}.count \\
diff --git a/modules/nf-core/kallistobustools/count/meta.yml b/modules/nf-core/kallistobustools/count/meta.yml
index c8763343..4a5d4b88 100644
--- a/modules/nf-core/kallistobustools/count/meta.yml
+++ b/modules/nf-core/kallistobustools/count/meta.yml
@@ -38,8 +38,8 @@ input:
       pattern: "*.{cdna_t2c.txt}"
   - t2c:
       type: file
-      description: kb ref's c2 unprocessed_t2c file
-      pattern: "*.{unprocessed_t2c.txt}"
+      description: kb ref's c2 intron_t2c file
+      pattern: "*.{intron_t2c.txt}"
   - workflow_mode:
       type: string
       description: String value defining workflow to use, can be one of "standard", "nac", "lamanno" (obsolete)
diff --git a/modules/nf-core/kallistobustools/ref/environment.yml b/modules/nf-core/kallistobustools/ref/environment.yml
index 62942e01..82aafedb 100644
--- a/modules/nf-core/kallistobustools/ref/environment.yml
+++ b/modules/nf-core/kallistobustools/ref/environment.yml
@@ -5,4 +5,5 @@ channels:
   - defaults
 dependencies:
   - bioconda::kb-python=0.28.2
-  - conda-forge::requests>=2.23.0
\ No newline at end of file
+  - conda-forge::requests>=2.23.0
+  
\ No newline at end of file
diff --git a/modules/nf-core/kallistobustools/ref/main.nf b/modules/nf-core/kallistobustools/ref/main.nf
index 989f86f3..759e8663 100644
--- a/modules/nf-core/kallistobustools/ref/main.nf
+++ b/modules/nf-core/kallistobustools/ref/main.nf
@@ -17,9 +17,9 @@ process KALLISTOBUSTOOLS_REF {
     path "kb_ref_out.idx" , emit: index
     path "t2g.txt"        , emit: t2g
     path "cdna.fa"        , emit: cdna
-    path "unprocessed.fa"      , optional:true, emit: unprocessed
+    path "intron.fa"      , optional:true, emit: intron
     path "cdna_t2c.txt"   , optional:true, emit: cdna_t2c
-    path "unprocessed_t2c.txt" , optional:true, emit: unprocessed_t2c
+    path "intron_t2c.txt" , optional:true, emit: intron_t2c
 
     when:
     task.ext.when == null || task.ext.when
@@ -49,9 +49,9 @@ process KALLISTOBUSTOOLS_REF {
             -i kb_ref_out.idx \\
             -g t2g.txt \\
             -f1 cdna.fa \\
-            -f2 unprocessed.fa \\
+            -f2 intron.fa \\
             -c1 cdna_t2c.txt \\
-            -c2 unprocessed_t2c.txt \\
+            -c2 intron_t2c.txt \\
             --workflow $workflow_mode \\
             $fasta \\
             $gtf
diff --git a/modules/nf-core/kallistobustools/ref/meta.yml b/modules/nf-core/kallistobustools/ref/meta.yml
index 1ca31c57..0c3f78a4 100644
--- a/modules/nf-core/kallistobustools/ref/meta.yml
+++ b/modules/nf-core/kallistobustools/ref/meta.yml
@@ -45,19 +45,19 @@ output:
       type: file
       description: cDNA fasta file
       pattern: "*cdna.{fa}"
-  - unprocessed:
+  - intron:
       type: file
-      description: Unprocessed fasta file
-      pattern: "*unprocessed.{fa}"
+      description: Intron fasta file
+      pattern: "*intron.{fa}"
   - cdna_t2c:
       type: file
       description: cDNA transcript to capture file
       pattern: "*cdna_t2c.{txt}"
-  - unprocessed_t2c:
+  - intron_t2c:
       type: file
-      description: Unprocessed transcript to capture file
-      pattern: "*unprocessed_t2c.{txt}"
+      description: Intron transcript to capture file
+      pattern: "*intron_t2c.{txt}"
 authors:
-  - "@flowuenne" 
+  - "@flowuenne"
 maintainers:
   - "@flowuenne"

From ac7e7cdfe24cf39e9b432d21e1a077e45da39684 Mon Sep 17 00:00:00 2001
From: gennadyFauna <153561808+gennadyFauna@users.noreply.github.com>
Date: Fri, 23 Feb 2024 13:00:01 -0800
Subject: [PATCH 16/34] Update nextflow_schema.json

---
 nextflow_schema.json | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/nextflow_schema.json b/nextflow_schema.json
index 10087c2c..2d204477 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -220,9 +220,9 @@
                 "kb_workflow": {
                     "type": "string",
                     "default": "standard",
-                    "description": "Type of workflow. Use `lamanno` for RNA velocity based on La Manno et al. 2018 logic. Use `nucleus` for RNA velocity on single-nucleus RNA-seq reads. Use `kite` for feature barcoding. Use `kite: 10xFB` for 10x Genomics Feature Barcoding technology. (default: standard)",
+                    "description": "Type of workflow. Use `nac` for an index type that can quantify nascent and mature RNA. Use `lamanno` for RNA velocity based on La Manno et al. 2018 logic. (default: standard)",
                     "fa_icon": "fas fa-rainbow",
-                    "enum": ["standard", "lamanno", "nucleus", "kite", "kite: 10xFB"]
+                    "enum": ["standard", "lamanno", "nac"]
                 }
             }
         },

From 8c4b8723b298a8f02c291e2f011f7e39660a0d11 Mon Sep 17 00:00:00 2001
From: gennadyFauna <153561808+gennadyFauna@users.noreply.github.com>
Date: Fri, 23 Feb 2024 14:35:01 -0800
Subject: [PATCH 17/34] Update main.nf

---
 modules/nf-core/kallistobustools/count/main.nf | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/modules/nf-core/kallistobustools/count/main.nf b/modules/nf-core/kallistobustools/count/main.nf
index ce5b5365..4679fe97 100644
--- a/modules/nf-core/kallistobustools/count/main.nf
+++ b/modules/nf-core/kallistobustools/count/main.nf
@@ -14,6 +14,7 @@ process KALLISTOBUSTOOLS_COUNT {
     path  t1c
     path  t2c
     val   technology
+    val   workflow_mode
 
     output:
     tuple val(meta), path ("*.count"), emit: count
@@ -38,6 +39,7 @@ process KALLISTOBUSTOOLS_COUNT {
         $cdna \\
         $intron \\
         -x $technology \\
+        --workflow $workflow_mode \\
         $args \\
         -o ${prefix}.count \\
         -m ${memory}G \\

From 8db2f9553da65c4814523a1bd548a41dc50b72f2 Mon Sep 17 00:00:00 2001
From: gennadyFauna <153561808+gennadyFauna@users.noreply.github.com>
Date: Fri, 23 Feb 2024 16:03:08 -0800
Subject: [PATCH 18/34] Update kallisto_bustools.nf

---
 subworkflows/local/kallisto_bustools.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/subworkflows/local/kallisto_bustools.nf b/subworkflows/local/kallisto_bustools.nf
index 7fdaf8ef..8b16dc56 100644
--- a/subworkflows/local/kallisto_bustools.nf
+++ b/subworkflows/local/kallisto_bustools.nf
@@ -34,7 +34,7 @@ workflow KALLISTO_BUSTOOLS {
         kallisto_index = KALLISTOBUSTOOLS_REF.out.index.collect()
         ch_versions = ch_versions.mix(KALLISTOBUSTOOLS_REF.out.versions)
         t1c = KALLISTOBUSTOOLS_REF.out.cdna_t2c.ifEmpty{ [] }
-        t2c = KALLISTOBUSTOOLS_REF.out.unprocessed_t2c.ifEmpty{ [] }
+        t2c = KALLISTOBUSTOOLS_REF.out.intron_t2c.ifEmpty{ [] }
     }
 
     /*

From a1fdcda8a13ade6c5218cd11f9068ab609b45746 Mon Sep 17 00:00:00 2001
From: gennadyFauna <153561808+gennadyFauna@users.noreply.github.com>
Date: Fri, 23 Feb 2024 16:09:08 -0800
Subject: [PATCH 19/34] Update kallisto_bustools.nf

---
 subworkflows/local/kallisto_bustools.nf | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/subworkflows/local/kallisto_bustools.nf b/subworkflows/local/kallisto_bustools.nf
index 8b16dc56..b6549094 100644
--- a/subworkflows/local/kallisto_bustools.nf
+++ b/subworkflows/local/kallisto_bustools.nf
@@ -46,7 +46,8 @@ workflow KALLISTO_BUSTOOLS {
         txp2gene,
         t1c,
         t2c,
-        protocol
+        protocol,
+        kb_workflow
     )
 
     ch_versions = ch_versions.mix(KALLISTOBUSTOOLS_COUNT.out.versions)

From 2aca75b5df3c90dc3284995b2c1713b9c8ec7747 Mon Sep 17 00:00:00 2001
From: gennadyFauna <153561808+gennadyFauna@users.noreply.github.com>
Date: Tue, 27 Feb 2024 11:39:50 -0800
Subject: [PATCH 20/34] docker container update

---
 modules/nf-core/kallistobustools/count/main.nf       | 4 ++--
 modules/nf-core/kallistobustools/count/meta.yml      | 2 +-
 modules/nf-core/kallistobustools/ref/environment.yml | 1 -
 modules/nf-core/kallistobustools/ref/main.nf         | 4 ++--
 modules/nf-core/kallistobustools/ref/meta.yml        | 2 +-
 5 files changed, 6 insertions(+), 7 deletions(-)

diff --git a/modules/nf-core/kallistobustools/count/main.nf b/modules/nf-core/kallistobustools/count/main.nf
index 4679fe97..67ad5812 100644
--- a/modules/nf-core/kallistobustools/count/main.nf
+++ b/modules/nf-core/kallistobustools/count/main.nf
@@ -4,8 +4,8 @@ process KALLISTOBUSTOOLS_COUNT {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/kb-python:0.28.2--pyhdfd78af_0' :
-        'biocontainers/kb-python:0.28.2--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/kb-python:0.28.2--pyhdfd78af_2' :
+        'biocontainers/kb-python:0.28.2--pyhdfd78af_2' }"
 
     input:
     tuple val(meta), path(reads)
diff --git a/modules/nf-core/kallistobustools/count/meta.yml b/modules/nf-core/kallistobustools/count/meta.yml
index 4a5d4b88..55d5dc6c 100644
--- a/modules/nf-core/kallistobustools/count/meta.yml
+++ b/modules/nf-core/kallistobustools/count/meta.yml
@@ -12,7 +12,7 @@ tools:
       homepage: https://www.kallistobus.tools/
       documentation: https://kb-python.readthedocs.io/en/latest/index.html
       tool_dev_url: https://github.com/pachterlab/kb_python
-      licence: MIT License
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/kallistobustools/ref/environment.yml b/modules/nf-core/kallistobustools/ref/environment.yml
index 82aafedb..6ae07a8c 100644
--- a/modules/nf-core/kallistobustools/ref/environment.yml
+++ b/modules/nf-core/kallistobustools/ref/environment.yml
@@ -6,4 +6,3 @@ channels:
 dependencies:
   - bioconda::kb-python=0.28.2
   - conda-forge::requests>=2.23.0
-  
\ No newline at end of file
diff --git a/modules/nf-core/kallistobustools/ref/main.nf b/modules/nf-core/kallistobustools/ref/main.nf
index 759e8663..702317d3 100644
--- a/modules/nf-core/kallistobustools/ref/main.nf
+++ b/modules/nf-core/kallistobustools/ref/main.nf
@@ -4,8 +4,8 @@ process KALLISTOBUSTOOLS_REF {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/kb-python:0.28.2--pyhdfd78af_0' :
-        'biocontainers/kb-python:0.28.2--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/kb-python:0.28.2--pyhdfd78af_2' :
+        'biocontainers/kb-python:0.28.2--pyhdfd78af_2' }"
 
     input:
     path fasta
diff --git a/modules/nf-core/kallistobustools/ref/meta.yml b/modules/nf-core/kallistobustools/ref/meta.yml
index 0c3f78a4..64deab9b 100644
--- a/modules/nf-core/kallistobustools/ref/meta.yml
+++ b/modules/nf-core/kallistobustools/ref/meta.yml
@@ -14,7 +14,7 @@ tools:
       documentation: https://kb-python.readthedocs.io/en/latest/index.html
       tool_dev_url: https://github.com/pachterlab/kb_python
       doi: "10.22002/D1.1876"
-      licence: MIT License
+      licence: ["MIT"]
 input:
   - fasta:
       type: file

From 0f5609325d0a55adb6e7a3283bedba07e7912873 Mon Sep 17 00:00:00 2001
From: gennadyFauna <153561808+gennadyFauna@users.noreply.github.com>
Date: Tue, 27 Feb 2024 12:05:48 -0800
Subject: [PATCH 21/34] manually updated md5s

this is not a real snapshot
---
 tests/main_pipeline_kallisto.test.snap | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

diff --git a/tests/main_pipeline_kallisto.test.snap b/tests/main_pipeline_kallisto.test.snap
index b0fb50bb..94a64ad8 100644
--- a/tests/main_pipeline_kallisto.test.snap
+++ b/tests/main_pipeline_kallisto.test.snap
@@ -20,15 +20,17 @@
                 "name": "workflow",
                 "success": true
             },
-            "cells_x_genes.barcodes.txt:md5,18be561873e435d4587f6b3f95a0e301",
+            "cells_x_genes.barcodes.txt:md5,72d78bb1c1ee7cb174520b30f695aa48",
+            "cells_x_genes.genes.names.txt:md5,a27831417ff4ed049d5b46012b270f4d",
             "cells_x_genes.genes.txt:md5,acd9d00120f52031974b2add3e7521b6",
-            "cells_x_genes.mtx:md5,37d2cd8c712f9c70463e87485bf6cd36",
-            "cells_x_genes.barcodes.txt:md5,488437e1f5477243697efb93366e5676",
+            "cells_x_genes.mtx:md5,894d60da192e3788de11fa8fc1fa711d",
+            "cells_x_genes.barcodes.txt:md5,a8cf7ea4b2d075296a94bf066a64b7a4",
+            "cells_x_genes.genes.names.txt:md5,a27831417ff4ed049d5b46012b270f4d",
             "cells_x_genes.genes.txt:md5,acd9d00120f52031974b2add3e7521b6",
-            "cells_x_genes.mtx:md5,af90e05b404490f6cb133ab7f62949f8",
-            "Sample_X_matrix.rds:md5,f0e43f69403f4b2e7704065421592ad0",
-            "Sample_Y_matrix.rds:md5,61809156e64dbdaf254cbc1c3456588e"
+            "cells_x_genes.mtx:md5,abd83de117204d0a77df3c92d00cc025",
+            "Sample_X_matrix.rds:md5,294781892964ed3c06f5c02124bb17b3",
+            "Sample_Y_matrix.rds:md5,b950e59c61ad3fdeb7293a1e5bfcd313"
         ],
-        "timestamp": "2024-01-23T12:19:47.921508953"
+        "timestamp": "2024-02-27T12:19:47.921508953"
     }
 }
\ No newline at end of file

From aae5fc5f618d1a4ccd40428d14050d838876f7fe Mon Sep 17 00:00:00 2001
From: gennadyFauna <153561808+gennadyFauna@users.noreply.github.com>
Date: Tue, 27 Feb 2024 12:19:56 -0800
Subject: [PATCH 22/34] Update main_pipeline_kallisto.test.snap

---
 tests/main_pipeline_kallisto.test.snap | 2 --
 1 file changed, 2 deletions(-)

diff --git a/tests/main_pipeline_kallisto.test.snap b/tests/main_pipeline_kallisto.test.snap
index 94a64ad8..867947ec 100644
--- a/tests/main_pipeline_kallisto.test.snap
+++ b/tests/main_pipeline_kallisto.test.snap
@@ -21,11 +21,9 @@
                 "success": true
             },
             "cells_x_genes.barcodes.txt:md5,72d78bb1c1ee7cb174520b30f695aa48",
-            "cells_x_genes.genes.names.txt:md5,a27831417ff4ed049d5b46012b270f4d",
             "cells_x_genes.genes.txt:md5,acd9d00120f52031974b2add3e7521b6",
             "cells_x_genes.mtx:md5,894d60da192e3788de11fa8fc1fa711d",
             "cells_x_genes.barcodes.txt:md5,a8cf7ea4b2d075296a94bf066a64b7a4",
-            "cells_x_genes.genes.names.txt:md5,a27831417ff4ed049d5b46012b270f4d",
             "cells_x_genes.genes.txt:md5,acd9d00120f52031974b2add3e7521b6",
             "cells_x_genes.mtx:md5,abd83de117204d0a77df3c92d00cc025",
             "Sample_X_matrix.rds:md5,294781892964ed3c06f5c02124bb17b3",

From 740a5dc6254f122b94816b43706cf84cd94cf189 Mon Sep 17 00:00:00 2001
From: gennadyFauna <153561808+gennadyFauna@users.noreply.github.com>
Date: Tue, 27 Feb 2024 13:01:57 -0800
Subject: [PATCH 23/34] update mtx construction

mtx should take in nascent/ambiguous/mature matrices.
The genes.names txt contains gene names, which are typically what is desired (e.g. cellranger has names rather than IDs)
---
 modules/local/mtx_to_h5ad.nf | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/modules/local/mtx_to_h5ad.nf b/modules/local/mtx_to_h5ad.nf
index 84d98608..043febf1 100644
--- a/modules/local/mtx_to_h5ad.nf
+++ b/modules/local/mtx_to_h5ad.nf
@@ -27,7 +27,7 @@ process MTX_TO_H5AD {
     if (params.aligner == 'kallisto') {
         mtx_matrix   = "*count/counts_unfiltered/*.mtx"
         barcodes_tsv = "*count/counts_unfiltered/*.barcodes.txt"
-        features_tsv = "*count/counts_unfiltered/*.genes.txt"
+        features_tsv = "*count/counts_unfiltered/*.genes.names.txt"
     } else if (params.aligner == 'alevin') {
         mtx_matrix   = "*_alevin_results/af_quant/alevin/quants_mat.mtx"
         barcodes_tsv = "*_alevin_results/af_quant/alevin/quants_mat_rows.txt"
@@ -54,13 +54,13 @@ process MTX_TO_H5AD {
     else if (params.aligner == 'kallisto' && params.kb_workflow != 'standard')
     """
     # convert file types
-    for input_type in spliced unspliced ; do
+    for input_type in nascent ambiguous mature ; do
         mtx_to_h5ad.py \\
             --aligner ${params.aligner} \\
             --sample ${meta.id} \\
-            --input *count/counts_unfiltered/\${input_type}.mtx \\
-            --barcode *count/counts_unfiltered/\${input_type}.barcodes.txt \\
-            --feature *count/counts_unfiltered/\${input_type}.genes.txt \\
+            --input *count/counts_unfiltered/cells_x_genes.\${input_type}.mtx \\
+            --barcode *count/counts_unfiltered/cells_x_genes.\${input_type}.barcodes.txt \\
+            --feature *count/counts_unfiltered/cells_x_genes.\${input_type}.genes.names.txt \\
             --txp2gene ${txp2gene} \\
             --star_index ${star_index} \\
             --out ${meta.id}/${meta.id}_\${input_type}_matrix.h5ad ;

From e7f59949be73f0a045d16ab266b390a9c5bab95e Mon Sep 17 00:00:00 2001
From: gennadyFauna <153561808+gennadyFauna@users.noreply.github.com>
Date: Tue, 27 Feb 2024 13:22:22 -0800
Subject: [PATCH 24/34] update seurat too

---
 modules/local/mtx_to_seurat.nf | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/modules/local/mtx_to_seurat.nf b/modules/local/mtx_to_seurat.nf
index d83575a4..04710f37 100644
--- a/modules/local/mtx_to_seurat.nf
+++ b/modules/local/mtx_to_seurat.nf
@@ -26,7 +26,7 @@ process MTX_TO_SEURAT {
     } else if (params.aligner == "kallisto") {
         matrix   = "*count/counts_unfiltered/*.mtx"
         barcodes = "*count/counts_unfiltered/*.barcodes.txt"
-        features = "*count/counts_unfiltered/*.genes.txt"
+        features = "*count/counts_unfiltered/*.genes.names.txt"
     } else if (params.aligner == "alevin") {
         matrix   = "*_alevin_results/af_quant/alevin/quants_mat.mtx"
         barcodes = "*_alevin_results/af_quant/alevin/quants_mat_rows.txt"
@@ -43,11 +43,11 @@ process MTX_TO_SEURAT {
     if (params.aligner == 'kallisto' && params.kb_workflow != 'standard')
     """
     # convert file types
-    for input_type in spliced unspliced ; do
+    for input_type in nascent ambiguous mature ; do
         mtx_to_seurat.R \\
-            *count/counts_unfiltered/\${input_type}.mtx \\
-            *count/counts_unfiltered/\${input_type}.barcodes.txt \\
-            *count/counts_unfiltered/\${input_type}.genes.txt \\
+            *count/counts_unfiltered/cells_x_genes.\${input_type}.mtx \\
+            *count/counts_unfiltered/cells_x_genes.\${input_type}.barcodes.txt \\
+            *count/counts_unfiltered/cells_x_genes.\${input_type}.genes.names.txt \\
             ${meta.id}/${meta.id}_\${input_type}_matrix.rds \\
             ${aligner}
     done

From 25ecada467c7a43d9b6450d25523f4d06fcadff2 Mon Sep 17 00:00:00 2001
From: gennadyFauna <153561808+gennadyFauna@users.noreply.github.com>
Date: Tue, 27 Feb 2024 13:40:33 -0800
Subject: [PATCH 25/34] this must have gotten fixed a few kb versions ago

---
 modules/local/mtx_to_h5ad.nf   | 2 +-
 modules/local/mtx_to_seurat.nf | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/local/mtx_to_h5ad.nf b/modules/local/mtx_to_h5ad.nf
index 043febf1..7bde6e79 100644
--- a/modules/local/mtx_to_h5ad.nf
+++ b/modules/local/mtx_to_h5ad.nf
@@ -59,7 +59,7 @@ process MTX_TO_H5AD {
             --aligner ${params.aligner} \\
             --sample ${meta.id} \\
             --input *count/counts_unfiltered/cells_x_genes.\${input_type}.mtx \\
-            --barcode *count/counts_unfiltered/cells_x_genes.\${input_type}.barcodes.txt \\
+            --barcode $barcodes_tsv \\
             --feature *count/counts_unfiltered/cells_x_genes.\${input_type}.genes.names.txt \\
             --txp2gene ${txp2gene} \\
             --star_index ${star_index} \\
diff --git a/modules/local/mtx_to_seurat.nf b/modules/local/mtx_to_seurat.nf
index 04710f37..a9ff508f 100644
--- a/modules/local/mtx_to_seurat.nf
+++ b/modules/local/mtx_to_seurat.nf
@@ -46,7 +46,7 @@ process MTX_TO_SEURAT {
     for input_type in nascent ambiguous mature ; do
         mtx_to_seurat.R \\
             *count/counts_unfiltered/cells_x_genes.\${input_type}.mtx \\
-            *count/counts_unfiltered/cells_x_genes.\${input_type}.barcodes.txt \\
+            $barcodes_tsv \\
             *count/counts_unfiltered/cells_x_genes.\${input_type}.genes.names.txt \\
             ${meta.id}/${meta.id}_\${input_type}_matrix.rds \\
             ${aligner}

From 072d187a29b1cd6c5f81bfa599b64920e0599ebb Mon Sep 17 00:00:00 2001
From: gennadyFauna <153561808+gennadyFauna@users.noreply.github.com>
Date: Tue, 27 Feb 2024 13:49:26 -0800
Subject: [PATCH 26/34] ...and the R changes have to be updated in md5

---
 tests/main_pipeline_kallisto.test.snap | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/main_pipeline_kallisto.test.snap b/tests/main_pipeline_kallisto.test.snap
index 867947ec..00fbb2b2 100644
--- a/tests/main_pipeline_kallisto.test.snap
+++ b/tests/main_pipeline_kallisto.test.snap
@@ -26,8 +26,8 @@
             "cells_x_genes.barcodes.txt:md5,a8cf7ea4b2d075296a94bf066a64b7a4",
             "cells_x_genes.genes.txt:md5,acd9d00120f52031974b2add3e7521b6",
             "cells_x_genes.mtx:md5,abd83de117204d0a77df3c92d00cc025",
-            "Sample_X_matrix.rds:md5,294781892964ed3c06f5c02124bb17b3",
-            "Sample_Y_matrix.rds:md5,b950e59c61ad3fdeb7293a1e5bfcd313"
+            "Sample_X_matrix.rds:md5,0938f4189b7a7fd1030abfcee798741c",
+            "Sample_Y_matrix.rds:md5,93c12abe283ab37c5f37e5cd3cb25302"
         ],
         "timestamp": "2024-02-27T12:19:47.921508953"
     }

From e006cdf2255ca793b303f7072b8c34687ac70909 Mon Sep 17 00:00:00 2001
From: gennadyFauna <153561808+gennadyFauna@users.noreply.github.com>
Date: Tue, 27 Feb 2024 13:53:28 -0800
Subject: [PATCH 27/34] correcting var

---
 modules/local/mtx_to_seurat.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/local/mtx_to_seurat.nf b/modules/local/mtx_to_seurat.nf
index a9ff508f..ac21e639 100644
--- a/modules/local/mtx_to_seurat.nf
+++ b/modules/local/mtx_to_seurat.nf
@@ -46,7 +46,7 @@ process MTX_TO_SEURAT {
     for input_type in nascent ambiguous mature ; do
         mtx_to_seurat.R \\
             *count/counts_unfiltered/cells_x_genes.\${input_type}.mtx \\
-            $barcodes_tsv \\
+            $barcodes \\
             *count/counts_unfiltered/cells_x_genes.\${input_type}.genes.names.txt \\
             ${meta.id}/${meta.id}_\${input_type}_matrix.rds \\
             ${aligner}

From 0187f8c2c036f301005450eaa635c6640ab610e8 Mon Sep 17 00:00:00 2001
From: gennadyFauna <153561808+gennadyFauna@users.noreply.github.com>
Date: Tue, 27 Feb 2024 14:16:38 -0800
Subject: [PATCH 28/34] features too

---
 modules/local/mtx_to_h5ad.nf   | 2 +-
 modules/local/mtx_to_seurat.nf | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/local/mtx_to_h5ad.nf b/modules/local/mtx_to_h5ad.nf
index 7bde6e79..c991b695 100644
--- a/modules/local/mtx_to_h5ad.nf
+++ b/modules/local/mtx_to_h5ad.nf
@@ -60,7 +60,7 @@ process MTX_TO_H5AD {
             --sample ${meta.id} \\
             --input *count/counts_unfiltered/cells_x_genes.\${input_type}.mtx \\
             --barcode $barcodes_tsv \\
-            --feature *count/counts_unfiltered/cells_x_genes.\${input_type}.genes.names.txt \\
+            --feature $features_tsv \\
             --txp2gene ${txp2gene} \\
             --star_index ${star_index} \\
             --out ${meta.id}/${meta.id}_\${input_type}_matrix.h5ad ;
diff --git a/modules/local/mtx_to_seurat.nf b/modules/local/mtx_to_seurat.nf
index ac21e639..82ee63cd 100644
--- a/modules/local/mtx_to_seurat.nf
+++ b/modules/local/mtx_to_seurat.nf
@@ -47,7 +47,7 @@ process MTX_TO_SEURAT {
         mtx_to_seurat.R \\
             *count/counts_unfiltered/cells_x_genes.\${input_type}.mtx \\
             $barcodes \\
-            *count/counts_unfiltered/cells_x_genes.\${input_type}.genes.names.txt \\
+            $features \\
             ${meta.id}/${meta.id}_\${input_type}_matrix.rds \\
             ${aligner}
     done

From 35dc9737fb68906e1ae664765411c06eb36805d2 Mon Sep 17 00:00:00 2001
From: EC2 Default User <ec2-user@ip-172-31-6-209.us-west-2.compute.internal>
Date: Mon, 4 Mar 2024 17:23:34 +0000
Subject: [PATCH 29/34] version bump

---
 .nf-test.log                                  |  17 +++
 modules.json                                  |  70 ++++++---
 .../nf-core/kallistobustools/count/main.nf    |  18 ++-
 .../kallistobustools/count/tests/main.nf.test |  98 +++++++++++++
 .../count/tests/main.nf.test.snap             | 100 +++++++++++++
 .../count/tests/nextflow.config               |   5 +
 .../kallistobustools/count/tests/tags.yml     |   2 +
 modules/nf-core/kallistobustools/ref/main.nf  |  28 ++++
 .../kallistobustools/ref/tests/main.nf.test   | 120 ++++++++++++++++
 .../ref/tests/main.nf.test.snap               | 136 ++++++++++++++++++
 .../kallistobustools/ref/tests/tags.yml       |   2 +
 tests/.nf-test.log                            |  21 +++
 12 files changed, 595 insertions(+), 22 deletions(-)
 create mode 100644 .nf-test.log
 create mode 100644 modules/nf-core/kallistobustools/count/tests/main.nf.test
 create mode 100644 modules/nf-core/kallistobustools/count/tests/main.nf.test.snap
 create mode 100644 modules/nf-core/kallistobustools/count/tests/nextflow.config
 create mode 100644 modules/nf-core/kallistobustools/count/tests/tags.yml
 create mode 100644 modules/nf-core/kallistobustools/ref/tests/main.nf.test
 create mode 100644 modules/nf-core/kallistobustools/ref/tests/main.nf.test.snap
 create mode 100644 modules/nf-core/kallistobustools/ref/tests/tags.yml
 create mode 100644 tests/.nf-test.log

diff --git a/.nf-test.log b/.nf-test.log
new file mode 100644
index 00000000..ca137888
--- /dev/null
+++ b/.nf-test.log
@@ -0,0 +1,17 @@
+Feb-27 21:54:16.881 [main] INFO  com.askimed.nf.test.App - nf-test 0.8.4
+Feb-27 21:54:16.895 [main] INFO  com.askimed.nf.test.App - Arguments: [test, tests/main_pipeline_kallisto.test, --update-snapshot]
+Feb-27 21:54:17.590 [main] INFO  com.askimed.nf.test.App - Nextflow Version: 23.10.1
+Feb-27 21:54:17.592 [main] INFO  com.askimed.nf.test.commands.RunTestsCommand - Load config from file /home/ec2-user/scrnaseq/nf-test.config...
+Feb-27 21:54:17.887 [main] INFO  com.askimed.nf.test.commands.RunTestsCommand - Detected 1 test files.
+Feb-27 21:54:18.162 [main] INFO  com.askimed.nf.test.config.FileStaging - Copy directory '/home/ec2-user/scrnaseq/bin' to '/home/ec2-user/scrnaseq/.nf-test/tests/72e0d0f6b834ab79755c0f97ef8c4ca8/meta/bin'
+Feb-27 21:54:18.164 [main] INFO  com.askimed.nf.test.config.FileStaging - Copy directory '/home/ec2-user/scrnaseq/lib' to '/home/ec2-user/scrnaseq/.nf-test/tests/72e0d0f6b834ab79755c0f97ef8c4ca8/meta/lib'
+Feb-27 21:54:18.164 [main] INFO  com.askimed.nf.test.config.FileStaging - Copy directory '/home/ec2-user/scrnaseq/assets' to '/home/ec2-user/scrnaseq/.nf-test/tests/72e0d0f6b834ab79755c0f97ef8c4ca8/meta/assets'
+Feb-27 21:54:18.171 [main] DEBUG com.askimed.nf.test.core.AbstractTest - Stage 0 user provided files...
+Feb-27 21:54:18.174 [main] INFO  com.askimed.nf.test.core.TestExecutionEngine - Started test plan
+Feb-27 21:54:18.174 [main] INFO  com.askimed.nf.test.core.TestExecutionEngine - Running testsuite 'Test Workflow main.nf' from file '/home/ec2-user/scrnaseq/tests/main_pipeline_kallisto.test'.
+Feb-27 21:54:18.174 [main] INFO  com.askimed.nf.test.core.TestExecutionEngine - Run test '72e0d0f6: test-dataset_kallisto_aligner'. type: com.askimed.nf.test.lang.pipeline.PipelineTest
+Feb-27 21:55:36.281 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Load snapshots from file '/home/ec2-user/scrnaseq/tests/main_pipeline_kallisto.test.snap'
+Feb-27 21:55:36.305 [main] DEBUG com.askimed.nf.test.lang.extensions.Snapshot - Snapshots 'test-dataset_kallisto_aligner' match.
+Feb-27 21:55:36.306 [main] INFO  com.askimed.nf.test.core.TestExecutionEngine - Test '72e0d0f6: test-dataset_kallisto_aligner' finished. status: PASSED
+Feb-27 21:55:36.308 [main] INFO  com.askimed.nf.test.core.TestExecutionEngine - Testsuite 'Test Workflow main.nf' finished. snapshot file: true, skipped tests: false, failed tests: false
+Feb-27 21:55:36.308 [main] INFO  com.askimed.nf.test.core.TestExecutionEngine - Executed 1 tests. 0 tests failed. Done!
diff --git a/modules.json b/modules.json
index c71a0499..51864fc4 100644
--- a/modules.json
+++ b/modules.json
@@ -8,85 +8,117 @@
                     "cellranger/count": {
                         "branch": "master",
                         "git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "cellranger/mkgtf": {
                         "branch": "master",
                         "git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "cellranger/mkref": {
                         "branch": "master",
                         "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "cellrangerarc/count": {
                         "branch": "master",
                         "git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "cellrangerarc/mkgtf": {
                         "branch": "master",
                         "git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "cellrangerarc/mkref": {
                         "branch": "master",
                         "git_sha": "4196b1b2e7ce265892f3979eabf7a9ddc030702f",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
                         "git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "fastqc": {
                         "branch": "master",
                         "git_sha": "f4ae1d942bd50c5c0b9bd2de1393ce38315ba57c",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "gffread": {
                         "branch": "master",
                         "git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "gunzip": {
                         "branch": "master",
                         "git_sha": "3a5fef109d113b4997c9822198664ca5f2716208",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "kallistobustools/count": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
-                        "installed_by": ["modules"]
+                        "git_sha": "de8215983defba48cd81961d620a9e844f11c7e7",
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "kallistobustools/ref": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
-                        "installed_by": ["modules"]
+                        "git_sha": "de8215983defba48cd81961d620a9e844f11c7e7",
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "multiqc": {
                         "branch": "master",
                         "git_sha": "9e71d8519dfbfc328c078bba14d4bd4c99e39a94",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "star/genomegenerate": {
                         "branch": "master",
                         "git_sha": "a21faa6a3481af92a343a10926f59c189a2c16c9",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "universc": {
                         "branch": "master",
                         "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "unzip": {
                         "branch": "master",
                         "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     }
                 }
             }
         }
     }
-}
+}
\ No newline at end of file
diff --git a/modules/nf-core/kallistobustools/count/main.nf b/modules/nf-core/kallistobustools/count/main.nf
index 67ad5812..841ea2fe 100644
--- a/modules/nf-core/kallistobustools/count/main.nf
+++ b/modules/nf-core/kallistobustools/count/main.nf
@@ -17,9 +17,9 @@ process KALLISTOBUSTOOLS_COUNT {
     val   workflow_mode
 
     output:
-    tuple val(meta), path ("*.count"), emit: count
-    path "versions.yml"              , emit: versions
-    path "*.count/*/*.mtx"           , emit: matrix //Ensure that kallisto finished and produced outputs
+    tuple val(meta), path ("*.count")   , emit: count
+    path "versions.yml"                 , emit: versions
+    path "*.count/*/*.mtx"              , emit: matrix //Ensure that kallisto finished and produced outputs
 
     when:
     task.ext.when == null || task.ext.when
@@ -50,4 +50,16 @@ process KALLISTOBUSTOOLS_COUNT {
         kallistobustools: \$(echo \$(kb --version 2>&1) | sed 's/^.*kb_python //;s/positional arguments.*\$//')
     END_VERSIONS
     """
+
+    stub:
+    def prefix  = task.ext.prefix ?: "${meta.id}"
+    """
+    mkdir -p ${prefix}.count/counts_unfiltered/
+    touch ${prefix}.count/counts_unfiltered/cells_x_genes.mtx
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        kallistobustools: \$(echo \$(kb --version 2>&1) | sed 's/^.*kb_python //;s/positional arguments.*\$//')
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/kallistobustools/count/tests/main.nf.test b/modules/nf-core/kallistobustools/count/tests/main.nf.test
new file mode 100644
index 00000000..550001f9
--- /dev/null
+++ b/modules/nf-core/kallistobustools/count/tests/main.nf.test
@@ -0,0 +1,98 @@
+nextflow_process {
+
+    name "Test Process KALLISTOBUSTOOLS_COUNT"
+    script "../main.nf"
+    process "KALLISTOBUSTOOLS_COUNT"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "kallistobustools"
+    tag "kallistobustools/count"
+    tag "kallistobustools/ref"
+
+    setup {
+        run("KALLISTOBUSTOOLS_REF") {
+            script "../../ref/main.nf"
+            process {
+                """
+                input[0] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true)
+                input[2] = "standard"
+                """
+            }
+        }
+    }
+
+    test("genome.fasta + genome.gtf + '10X3' + 'standard'") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of(
+                    [
+                        [id:'test'], // meta map
+                        [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc_cmo/fastqs/gex_1/subsampled_SC3_v3_NextGem_DI_CellPlex_Human_PBMC_10K_1_gex_S2_L001_R1_001.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc_cmo/fastqs/gex_1/subsampled_SC3_v3_NextGem_DI_CellPlex_Human_PBMC_10K_1_gex_S2_L001_R2_001.fastq.gz', checkIfExists: true)
+                        ]
+                    ]
+                )
+                input[1] = KALLISTOBUSTOOLS_REF.out.index
+                input[2] = KALLISTOBUSTOOLS_REF.out.t2g
+                input[3] = KALLISTOBUSTOOLS_REF.out.cdna_t2c.ifEmpty{ [] }   // when empty the module doesn't run unless something is passed.
+                input[4] = KALLISTOBUSTOOLS_REF.out.intron_t2c.ifEmpty{ [] } // when empty the module doesn't run unless something is passed.
+                input[5] = "10XV3"
+                input[6] = "standard"
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.versions,
+                    process.out.matrix,
+                    path(process.out.count.get(0).get(1)).list().findAll { file(it.toString()).name != "run_info.json" && file(it.toString()).name != "kb_info.json" },
+                    file(path(process.out.count.get(0).get(1)).list().find { file(it.toString()).name == "kb_info.json" }.toString()).readLines()[15..22],
+                    file(path(process.out.count.get(0).get(1)).list().find { file(it.toString()).name == "run_info.json" }.toString()).readLines()[0..9]
+                    ).match()
+                }
+            )
+        }
+    }
+
+    test("genome.fasta + genome.gtf + '10X3' + 'standard' - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of(
+                    [
+                        [id:'test'], // meta map
+                        [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc_cmo/fastqs/gex_1/subsampled_SC3_v3_NextGem_DI_CellPlex_Human_PBMC_10K_1_gex_S2_L001_R1_001.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc_cmo/fastqs/gex_1/subsampled_SC3_v3_NextGem_DI_CellPlex_Human_PBMC_10K_1_gex_S2_L001_R2_001.fastq.gz', checkIfExists: true)
+                        ]
+                    ]
+                )
+                input[1] = KALLISTOBUSTOOLS_REF.out.index
+                input[2] = KALLISTOBUSTOOLS_REF.out.t2g
+                input[3] = KALLISTOBUSTOOLS_REF.out.cdna_t2c.ifEmpty{ [] }   // when empty the module doesn't run unless something is passed.
+                input[4] = KALLISTOBUSTOOLS_REF.out.intron_t2c.ifEmpty{ [] } // when empty the module doesn't run unless something is passed.
+                input[5] = "10XV3"
+                input[6] = "standard"
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/kallistobustools/count/tests/main.nf.test.snap b/modules/nf-core/kallistobustools/count/tests/main.nf.test.snap
new file mode 100644
index 00000000..3378c3c1
--- /dev/null
+++ b/modules/nf-core/kallistobustools/count/tests/main.nf.test.snap
@@ -0,0 +1,100 @@
+{
+    "genome.fasta + genome.gtf + '10X3' + 'standard' - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            [
+                                "cells_x_genes.mtx:md5,d41d8cd98f00b204e9800998ecf8427e"
+                            ]
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,6ec06270afe0a7572c41567160d927d9"
+                ],
+                "2": [
+                    "cells_x_genes.mtx:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "count": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            [
+                                "cells_x_genes.mtx:md5,d41d8cd98f00b204e9800998ecf8427e"
+                            ]
+                        ]
+                    ]
+                ],
+                "matrix": [
+                    "cells_x_genes.mtx:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "versions": [
+                    "versions.yml:md5,6ec06270afe0a7572c41567160d927d9"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-01T15:48:45.775904562"
+    },
+    "genome.fasta + genome.gtf + '10X3' + 'standard'": {
+        "content": [
+            [
+                "versions.yml:md5,6ec06270afe0a7572c41567160d927d9"
+            ],
+            [
+                "cells_x_genes.mtx:md5,e12a45e7f7d6527f698dd9cb2e99ecd1"
+            ],
+            [
+                "10x_version3_whitelist.txt:md5,3d36d0a4021fd292b265e2b5e72aaaf3",
+                [
+                    "cells_x_genes.barcodes.txt:md5,41f7adaf43b60f2f4f62d6a7073688de",
+                    "cells_x_genes.genes.names.txt:md5,b29afa75be300c7f24fbd0740a66689b",
+                    "cells_x_genes.genes.txt:md5,fe6d5501923867b514a0447aa4b4995f",
+                    "cells_x_genes.mtx:md5,e12a45e7f7d6527f698dd9cb2e99ecd1"
+                ],
+                "inspect.json:md5,bafb47a58ac1bbf9be953f21c361d266",
+                "matrix.ec:md5,31a4c1a3e8e0c562b12f6569ffbf5459",
+                "output.bus:md5,d6fa0612a4a16eaf8a3e08bdc13ff49c",
+                "output.unfiltered.bus:md5,bf899b967657f612ba864188868d58cc",
+                "transcripts.txt:md5,23861cf43033e7c596e6989a88a3a373"
+            ],
+            [
+                "    \"commands\": [",
+                "        \"kallisto bus -i kb_ref_out.idx -o test.count -x 10XV3 -t 2 subsampled_SC3_v3_NextGem_DI_CellPlex_Human_PBMC_10K_1_gex_S2_L001_R1_001.fastq.gz subsampled_SC3_v3_NextGem_DI_CellPlex_Human_PBMC_10K_1_gex_S2_L001_R2_001.fastq.gz\",",
+                "        \"bustools sort -o test.count/tmp/output.s.bus -T test.count/tmp -t 2 -m 2G test.count/output.bus\",",
+                "        \"bustools inspect -o test.count/inspect.json -w test.count/10x_version3_whitelist.txt test.count/tmp/output.s.bus\",",
+                "        \"bustools correct -o test.count/tmp/output.s.c.bus -w test.count/10x_version3_whitelist.txt test.count/tmp/output.s.bus\",",
+                "        \"bustools sort -o test.count/output.unfiltered.bus -T test.count/tmp -t 2 -m 2G test.count/tmp/output.s.c.bus\",",
+                "        \"bustools count -o test.count/counts_unfiltered/cells_x_genes -g t2g.txt -e test.count/matrix.ec -t test.count/transcripts.txt --genecounts --umi-gene test.count/output.unfiltered.bus\"",
+                "    ],"
+            ],
+            [
+                "{",
+                "\t\"n_targets\": 12,",
+                "\t\"n_bootstraps\": 0,",
+                "\t\"n_processed\": 10000,",
+                "\t\"n_pseudoaligned\": 26,",
+                "\t\"n_unique\": 26,",
+                "\t\"p_pseudoaligned\": 0.3,",
+                "\t\"p_unique\": 0.3,",
+                "\t\"kallisto_version\": \"0.50.1\",",
+                "\t\"index_version\": 13,"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-01T15:48:24.476953631"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/kallistobustools/count/tests/nextflow.config b/modules/nf-core/kallistobustools/count/tests/nextflow.config
new file mode 100644
index 00000000..7a5cbfb4
--- /dev/null
+++ b/modules/nf-core/kallistobustools/count/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: KALLISTOBUSTOOLS_COUNT {
+        ext.args = '--cellranger -m 1'
+    }
+}
diff --git a/modules/nf-core/kallistobustools/count/tests/tags.yml b/modules/nf-core/kallistobustools/count/tests/tags.yml
new file mode 100644
index 00000000..9c432071
--- /dev/null
+++ b/modules/nf-core/kallistobustools/count/tests/tags.yml
@@ -0,0 +1,2 @@
+kallistobustools/count:
+  - "modules/nf-core/kallistobustools/count/**"
diff --git a/modules/nf-core/kallistobustools/ref/main.nf b/modules/nf-core/kallistobustools/ref/main.nf
index 702317d3..0b45203d 100644
--- a/modules/nf-core/kallistobustools/ref/main.nf
+++ b/modules/nf-core/kallistobustools/ref/main.nf
@@ -62,4 +62,32 @@ process KALLISTOBUSTOOLS_REF {
         END_VERSIONS
         """
     }
+
+    stub:
+    if (workflow_mode == "standard") {
+        """
+        touch kb_ref_out.idx \\
+        touch t2g.txt \\
+        touch cdna.fa
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            kallistobustools: \$(echo \$(kb --version 2>&1) | sed 's/^.*kb_python //;s/positional arguments.*\$//')
+        END_VERSIONS
+        """
+    } else {
+        """
+        touch kb_ref_out.idx \\
+        touch t2g.txt \\
+        touch cdna.fa
+        touch intron.fa \\
+        touch cdna_t2c.txt \\
+        touch intron_t2c.txt
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            kallistobustools: \$(echo \$(kb --version 2>&1) | sed 's/^.*kb_python //;s/positional arguments.*\$//')
+        END_VERSIONS
+        """
+    }
 }
diff --git a/modules/nf-core/kallistobustools/ref/tests/main.nf.test b/modules/nf-core/kallistobustools/ref/tests/main.nf.test
new file mode 100644
index 00000000..dc49d9ac
--- /dev/null
+++ b/modules/nf-core/kallistobustools/ref/tests/main.nf.test
@@ -0,0 +1,120 @@
+nextflow_process {
+
+    name "Test Process KALLISTOBUSTOOLS_REF"
+    script "../main.nf"
+    process "KALLISTOBUSTOOLS_REF"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "kallistobustools"
+    tag "kallistobustools/ref"
+
+    test("genome.fasta + genome.gtf + 'standard'") {
+
+        when {
+            process {
+                """
+                input[0] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true)
+                input[2] = "standard"
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.versions,
+                    process.out.t2g,
+                    process.out.cdna,
+                    process.out.intron,
+                    process.out.cdna_t2c,
+                    process.out.intron_t2c,
+                    ).match()
+                },
+                { assert file(process.out.index.get(0)).exists() }
+            )
+        }
+    }
+
+    test("genome.fasta + genome.gtf + 'nac'") {
+
+        when {
+            process {
+                """
+                input[0] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true)
+                input[2] = "nac"
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.versions,
+                    process.out.t2g,
+                    process.out.cdna,
+                    process.out.intron,
+                    process.out.cdna_t2c,
+                    process.out.intron_t2c,
+                    ).match()
+                },
+                { assert file(process.out.index.get(0)).exists() }
+            )
+        }
+    }
+
+    test("genome.fasta + genome.gtf + 'standard' - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true)
+                input[2] = "standard"
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("genome.fasta + genome.gtf + 'nac' - stub") {
+
+        when {
+            process {
+                """
+                input[0] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true)
+                input[2] = "nac"
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.versions,
+                    process.out.t2g,
+                    process.out.cdna,
+                    process.out.intron,
+                    process.out.cdna_t2c,
+                    process.out.intron_t2c,
+                    ).match()
+                },
+                { assert file(process.out.index.get(0)).exists() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/kallistobustools/ref/tests/main.nf.test.snap b/modules/nf-core/kallistobustools/ref/tests/main.nf.test.snap
new file mode 100644
index 00000000..9c2be8a7
--- /dev/null
+++ b/modules/nf-core/kallistobustools/ref/tests/main.nf.test.snap
@@ -0,0 +1,136 @@
+{
+    "genome.fasta + genome.gtf + 'standard'": {
+        "content": [
+            [
+                "versions.yml:md5,d3d08c3c5638ae540965f77b8178b3c1"
+            ],
+            [
+                "t2g.txt:md5,d1a8a22c59b9cb0bda39c0c9bb3f6afe"
+            ],
+            [
+                "cdna.fa:md5,7bca59288fab822451de250d2eee48dc"
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-29T23:37:43.739374859"
+    },
+    "genome.fasta + genome.gtf + 'nac'": {
+        "content": [
+            [
+                "versions.yml:md5,d3d08c3c5638ae540965f77b8178b3c1"
+            ],
+            [
+                "t2g.txt:md5,58591306b33bb948bac7b40f346d0cd7"
+            ],
+            [
+                "cdna.fa:md5,7bca59288fab822451de250d2eee48dc"
+            ],
+            [
+                "intron.fa:md5,1aad4e3f5d006f495cc6647fa0bbf6ff"
+            ],
+            [
+                "cdna_t2c.txt:md5,23861cf43033e7c596e6989a88a3a373"
+            ],
+            [
+                "intron_t2c.txt:md5,fe6d5501923867b514a0447aa4b4995f"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-29T23:37:59.436989671"
+    },
+    "genome.fasta + genome.gtf + 'standard' - stub": {
+        "content": [
+            {
+                "0": [
+                    "versions.yml:md5,d3d08c3c5638ae540965f77b8178b3c1"
+                ],
+                "1": [
+                    "kb_ref_out.idx:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "2": [
+                    "t2g.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "3": [
+                    "cdna.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "4": [
+                    
+                ],
+                "5": [
+                    
+                ],
+                "6": [
+                    
+                ],
+                "cdna": [
+                    "cdna.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "cdna_t2c": [
+                    
+                ],
+                "index": [
+                    "kb_ref_out.idx:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "intron": [
+                    
+                ],
+                "intron_t2c": [
+                    
+                ],
+                "t2g": [
+                    "t2g.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "versions": [
+                    "versions.yml:md5,d3d08c3c5638ae540965f77b8178b3c1"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-29T23:38:09.578411047"
+    },
+    "genome.fasta + genome.gtf + 'nac' - stub": {
+        "content": [
+            [
+                "versions.yml:md5,d3d08c3c5638ae540965f77b8178b3c1"
+            ],
+            [
+                "t2g.txt:md5,58591306b33bb948bac7b40f346d0cd7"
+            ],
+            [
+                "cdna.fa:md5,7bca59288fab822451de250d2eee48dc"
+            ],
+            [
+                "intron.fa:md5,1aad4e3f5d006f495cc6647fa0bbf6ff"
+            ],
+            [
+                "cdna_t2c.txt:md5,23861cf43033e7c596e6989a88a3a373"
+            ],
+            [
+                "intron_t2c.txt:md5,fe6d5501923867b514a0447aa4b4995f"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-29T23:38:25.355912473"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/kallistobustools/ref/tests/tags.yml b/modules/nf-core/kallistobustools/ref/tests/tags.yml
new file mode 100644
index 00000000..208c8d27
--- /dev/null
+++ b/modules/nf-core/kallistobustools/ref/tests/tags.yml
@@ -0,0 +1,2 @@
+kallistobustools/ref:
+  - "modules/nf-core/kallistobustools/ref/**"
diff --git a/tests/.nf-test.log b/tests/.nf-test.log
new file mode 100644
index 00000000..8251fc75
--- /dev/null
+++ b/tests/.nf-test.log
@@ -0,0 +1,21 @@
+Feb-27 21:54:09.971 [main] INFO  com.askimed.nf.test.App - nf-test 0.8.4
+Feb-27 21:54:09.988 [main] INFO  com.askimed.nf.test.App - Arguments: [test, tests/main_pipeline_kallisto.test, --update-snapshot]
+Feb-27 21:54:10.670 [main] INFO  com.askimed.nf.test.App - Nextflow Version: 23.10.1
+Feb-27 21:54:10.674 [main] WARN  com.askimed.nf.test.commands.RunTestsCommand - No nf-test config file found.
+Feb-27 21:54:10.674 [main] INFO  com.askimed.nf.test.commands.RunTestsCommand - Detected 1 test files.
+Feb-27 21:54:10.676 [main] ERROR com.askimed.nf.test.commands.RunTestsCommand - Running tests failed.
+java.lang.Exception: Test file '/home/ec2-user/scrnaseq/tests/tests/main_pipeline_kallisto.test' not found.
+	at com.askimed.nf.test.core.TestExecutionEngine.parse(TestExecutionEngine.java:116)
+	at com.askimed.nf.test.core.TestExecutionEngine.execute(TestExecutionEngine.java:159)
+	at com.askimed.nf.test.commands.RunTestsCommand.execute(RunTestsCommand.java:184)
+	at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:43)
+	at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:18)
+	at picocli.CommandLine.executeUserObject(CommandLine.java:1953)
+	at picocli.CommandLine.access$1300(CommandLine.java:145)
+	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2352)
+	at picocli.CommandLine$RunLast.handle(CommandLine.java:2346)
+	at picocli.CommandLine$RunLast.handle(CommandLine.java:2311)
+	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179)
+	at picocli.CommandLine.execute(CommandLine.java:2078)
+	at com.askimed.nf.test.App.run(App.java:44)
+	at com.askimed.nf.test.App.main(App.java:51)

From f12cfbbdc89ed0b65737c689f1ef80f7c4e51bdb Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Mon, 4 Mar 2024 19:14:39 +0000
Subject: [PATCH 30/34] [automated] Fix linting with Prettier

---
 modules.json | 66 ++++++++++++++--------------------------------------
 1 file changed, 17 insertions(+), 49 deletions(-)

diff --git a/modules.json b/modules.json
index 51864fc4..f6ae83cd 100644
--- a/modules.json
+++ b/modules.json
@@ -8,117 +8,85 @@
                     "cellranger/count": {
                         "branch": "master",
                         "git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "cellranger/mkgtf": {
                         "branch": "master",
                         "git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "cellranger/mkref": {
                         "branch": "master",
                         "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "cellrangerarc/count": {
                         "branch": "master",
                         "git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "cellrangerarc/mkgtf": {
                         "branch": "master",
                         "git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "cellrangerarc/mkref": {
                         "branch": "master",
                         "git_sha": "4196b1b2e7ce265892f3979eabf7a9ddc030702f",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
                         "git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "fastqc": {
                         "branch": "master",
                         "git_sha": "f4ae1d942bd50c5c0b9bd2de1393ce38315ba57c",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "gffread": {
                         "branch": "master",
                         "git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "gunzip": {
                         "branch": "master",
                         "git_sha": "3a5fef109d113b4997c9822198664ca5f2716208",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "kallistobustools/count": {
                         "branch": "master",
                         "git_sha": "de8215983defba48cd81961d620a9e844f11c7e7",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "kallistobustools/ref": {
                         "branch": "master",
                         "git_sha": "de8215983defba48cd81961d620a9e844f11c7e7",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
                         "git_sha": "9e71d8519dfbfc328c078bba14d4bd4c99e39a94",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "star/genomegenerate": {
                         "branch": "master",
                         "git_sha": "a21faa6a3481af92a343a10926f59c189a2c16c9",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "universc": {
                         "branch": "master",
                         "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "unzip": {
                         "branch": "master",
                         "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     }
                 }
             }
         }
     }
-}
\ No newline at end of file
+}

From fdda7a596fc4dd733976540c05558c5efceda67d Mon Sep 17 00:00:00 2001
From: Gregor Sturm <mail@gregor-sturm.de>
Date: Thu, 7 Mar 2024 12:39:28 +0100
Subject: [PATCH 31/34] Delete .nf-test.log

---
 .nf-test.log | 17 -----------------
 1 file changed, 17 deletions(-)
 delete mode 100644 .nf-test.log

diff --git a/.nf-test.log b/.nf-test.log
deleted file mode 100644
index ca137888..00000000
--- a/.nf-test.log
+++ /dev/null
@@ -1,17 +0,0 @@
-Feb-27 21:54:16.881 [main] INFO  com.askimed.nf.test.App - nf-test 0.8.4
-Feb-27 21:54:16.895 [main] INFO  com.askimed.nf.test.App - Arguments: [test, tests/main_pipeline_kallisto.test, --update-snapshot]
-Feb-27 21:54:17.590 [main] INFO  com.askimed.nf.test.App - Nextflow Version: 23.10.1
-Feb-27 21:54:17.592 [main] INFO  com.askimed.nf.test.commands.RunTestsCommand - Load config from file /home/ec2-user/scrnaseq/nf-test.config...
-Feb-27 21:54:17.887 [main] INFO  com.askimed.nf.test.commands.RunTestsCommand - Detected 1 test files.
-Feb-27 21:54:18.162 [main] INFO  com.askimed.nf.test.config.FileStaging - Copy directory '/home/ec2-user/scrnaseq/bin' to '/home/ec2-user/scrnaseq/.nf-test/tests/72e0d0f6b834ab79755c0f97ef8c4ca8/meta/bin'
-Feb-27 21:54:18.164 [main] INFO  com.askimed.nf.test.config.FileStaging - Copy directory '/home/ec2-user/scrnaseq/lib' to '/home/ec2-user/scrnaseq/.nf-test/tests/72e0d0f6b834ab79755c0f97ef8c4ca8/meta/lib'
-Feb-27 21:54:18.164 [main] INFO  com.askimed.nf.test.config.FileStaging - Copy directory '/home/ec2-user/scrnaseq/assets' to '/home/ec2-user/scrnaseq/.nf-test/tests/72e0d0f6b834ab79755c0f97ef8c4ca8/meta/assets'
-Feb-27 21:54:18.171 [main] DEBUG com.askimed.nf.test.core.AbstractTest - Stage 0 user provided files...
-Feb-27 21:54:18.174 [main] INFO  com.askimed.nf.test.core.TestExecutionEngine - Started test plan
-Feb-27 21:54:18.174 [main] INFO  com.askimed.nf.test.core.TestExecutionEngine - Running testsuite 'Test Workflow main.nf' from file '/home/ec2-user/scrnaseq/tests/main_pipeline_kallisto.test'.
-Feb-27 21:54:18.174 [main] INFO  com.askimed.nf.test.core.TestExecutionEngine - Run test '72e0d0f6: test-dataset_kallisto_aligner'. type: com.askimed.nf.test.lang.pipeline.PipelineTest
-Feb-27 21:55:36.281 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Load snapshots from file '/home/ec2-user/scrnaseq/tests/main_pipeline_kallisto.test.snap'
-Feb-27 21:55:36.305 [main] DEBUG com.askimed.nf.test.lang.extensions.Snapshot - Snapshots 'test-dataset_kallisto_aligner' match.
-Feb-27 21:55:36.306 [main] INFO  com.askimed.nf.test.core.TestExecutionEngine - Test '72e0d0f6: test-dataset_kallisto_aligner' finished. status: PASSED
-Feb-27 21:55:36.308 [main] INFO  com.askimed.nf.test.core.TestExecutionEngine - Testsuite 'Test Workflow main.nf' finished. snapshot file: true, skipped tests: false, failed tests: false
-Feb-27 21:55:36.308 [main] INFO  com.askimed.nf.test.core.TestExecutionEngine - Executed 1 tests. 0 tests failed. Done!

From 6b46540896052f43db7e91b5c4d6e95f85498013 Mon Sep 17 00:00:00 2001
From: Gregor Sturm <mail@gregor-sturm.de>
Date: Thu, 7 Mar 2024 12:40:45 +0100
Subject: [PATCH 32/34] Update nextflow_schema.json

---
 nextflow_schema.json | 1 -
 1 file changed, 1 deletion(-)

diff --git a/nextflow_schema.json b/nextflow_schema.json
index 0f1433c4..42599d59 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -237,7 +237,6 @@
                     "type": "string",
                     "description": "Specify a path to the intron transcripts-to-capture.",
                     "fa_icon": "fas fa-rainbow"
-                    "fa_icon": "fas fa-fish",
                     "format": "file-path",
                     "exists": true
                 },

From 904743e1f1e2ed62485f10135925ad33d6b306c3 Mon Sep 17 00:00:00 2001
From: Gregor Sturm <gregor.sturm@boehringer-ingelheim.com>
Date: Thu, 7 Mar 2024 12:46:52 +0100
Subject: [PATCH 33/34] Fix nextflow schema

---
 nextflow_schema.json | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/nextflow_schema.json b/nextflow_schema.json
index 42599d59..65b56954 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -224,7 +224,9 @@
                 "kallisto_index": {
                     "type": "string",
                     "description": "Specify a path to the precomputed Kallisto index.",
-                    "fa_icon": "fas fa-rainbow"
+                    "fa_icon": "fas fa-rainbow",
+                    "format": "file-path",
+                    "exists": true
                 },
                 "kb_t1c": {
                     "type": "string",
@@ -236,7 +238,7 @@
                 "kb_t2c": {
                     "type": "string",
                     "description": "Specify a path to the intron transcripts-to-capture.",
-                    "fa_icon": "fas fa-rainbow"
+                    "fa_icon": "fas fa-rainbow",
                     "format": "file-path",
                     "exists": true
                 },

From 600619f7eeff522b36523630dc6c60a1c0fd6227 Mon Sep 17 00:00:00 2001
From: Gregor Sturm <gregor.sturm@boehringer-ingelheim.com>
Date: Thu, 7 Mar 2024 12:50:46 +0100
Subject: [PATCH 34/34] Update changelog

---
 CHANGELOG.md         | 4 +++-
 nextflow_schema.json | 5 -----
 2 files changed, 3 insertions(+), 6 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index b42791db..a9d9a7e7 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,7 +5,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## v2.6.0dev - [date]
 
-- [[#91](https://github.com/nf-core/scrnaseq/issues/91)] - Change from pytests to nf-test
+- Change from pytests to nf-test ([#291](https://github.com/nf-core/scrnaseq/pull/291))
+- Update template to v2.13.1 ([#309](https://github.com/nf-core/scrnaseq/pull/309))
+- Update to kallisto|bustools v0.28.2 ([#294](https://github.com/nf-core/scrnaseq/pull/294))
 
 ## v2.5.1
 
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 65b56954..23f6e9b5 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -145,11 +145,6 @@
                     "default": "s3://ngi-igenomes/igenomes/",
                     "fa_icon": "fas fa-cloud-download-alt",
                     "hidden": true
-                },
-                "txp2gene": {
-                    "type": "string",
-                    "description": "Kallisto or Alevin gene mapping file.",
-                    "fa_icon": "fas map-marked-alt"
                 }
             }
         },