Merge pull request #120 from Daniel-VM/dev

Routine updating of installed modules and subworkflows
nf-core · Mar 22, 2024 · c1512ff · c1512ff
2 parents 6265523 + 9bd943a
commit c1512ff
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,10 +7,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Changed`
 
+- [#111](https://github.com/nf-core/bacass/pull/111) - Update nf-core/bacass to 2.12, and [#117](https://github.com/nf-core/bacass/pull/117) to 2.13.1 `TEMPLATE`.
+- [#120](https://github.com/nf-core/bacass/pull/120) - Update local and nf-core modules (version update an minnor code changes).
+
 ### `Added`
 
 - [#104](https://github.com/nf-core/bacass/pull/104), [#106](https://github.com/nf-core/bacass/pull/106) - Added dragonflye module and enbled draft genome polishing with short-reads.
-- [#111](https://github.com/nf-core/bacass/pull/111) - Update nf-core/bacass to 2.12, and [#117](https://github.com/nf-core/bacass/pull/117) to 2.13.1 `TEMPLATE`.
 
 ### `Fixed`
 

diff --git a/modules.json b/modules.json
@@ -7,12 +7,12 @@
                 "nf-core": {
                     "bakta/bakta": {
                         "branch": "master",
-                        "git_sha": "f05fa7c6753f92be861d606378860dcd5c828880",
+                        "git_sha": "9d0f89b445e1f5b2fb30476f4be9a8b519c07846",
                         "installed_by": ["modules"]
                     },
                     "bakta/baktadbdownload": {
                         "branch": "master",
-                        "git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc",
+                        "git_sha": "7c06e6820fa3918bc28a040e794f8a2b39fabadb",
                         "installed_by": ["modules"]
                     },
                     "canu": {
@@ -22,13 +22,13 @@
                     },
                     "dragonflye": {
                         "branch": "master",
-                        "git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc",
+                        "git_sha": "a3ae45e99f68e513b0feb8d5f27e2fdd0d0f083d",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/dragonflye/dragonflye.diff"
                     },
                     "fastp": {
                         "branch": "master",
-                        "git_sha": "003920c7f9a8ae19b69a97171922880220bedf56",
+                        "git_sha": "95cf5fe0194c7bf5cb0e3027a2eb7e7c89385080",
                         "installed_by": ["fastq_trim_fastp_fastqc"]
                     },
                     "fastqc": {
@@ -38,22 +38,22 @@
                     },
                     "gunzip": {
                         "branch": "master",
-                        "git_sha": "e06548bfa36ee31869b81041879dd6b3a83b1d57",
+                        "git_sha": "3a5fef109d113b4997c9822198664ca5f2716208",
                         "installed_by": ["modules"]
                     },
                     "kraken2/kraken2": {
                         "branch": "master",
-                        "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
+                        "git_sha": "653218e79ffa76fde20319e9062f8b8da5cf7555",
                         "installed_by": ["modules"]
                     },
                     "miniasm": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "minimap2/align": {
                         "branch": "master",
-                        "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
+                        "git_sha": "2c2d1cf80866dbd6dd0ea5d61ddd59533a72d41e",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
@@ -63,43 +63,43 @@
                     },
                     "nanoplot": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "a31407dfaf0cb0d04768d5cb439fc6f4523a6981",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/nanoplot/nanoplot.diff"
                     },
                     "porechop/porechop": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "1d68c7f248d1a480c5959548a9234602b771199e",
                         "installed_by": ["modules"]
                     },
                     "prokka": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "49ebda931c36c2b282f7958d00e1236b751f1031",
                         "installed_by": ["modules"]
                     },
                     "quast": {
                         "branch": "master",
-                        "git_sha": "344638191a5d6b3526556410819dfcf24e98039e",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "racon": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "samtools/index": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
                         "installed_by": ["modules"]
                     },
                     "samtools/sort": {
                         "branch": "master",
-                        "git_sha": "a0f7be95788366c1923171e358da7d049eb440f9",
+                        "git_sha": "4352dbdb09ec40db71e9b172b97a01dcf5622c26",
                         "installed_by": ["modules"]
                     },
                     "untar": {
                         "branch": "master",
-                        "git_sha": "d0b4fc03af52a1cc8c6fb4493b921b57352b1dd8",
+                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
                         "installed_by": ["modules"]
                     }
                 }

diff --git a/modules/local/dfast/environment.yml b/modules/local/dfast/environment.yml
@@ -0,0 +1,7 @@
+name: dfast
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::dfast=1.2.20
diff --git a/modules/local/dfast.nf → modules/local/dfast/main.nf b/modules/local/dfast.nf → modules/local/dfast/main.nf
@@ -2,7 +2,7 @@ process DFAST {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::dfast=1.2.20"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/dfast:1.2.20--h43eeafb_0' :
         'biocontainers/dfast:1.2.20--h43eeafb_0' }"

diff --git a/modules/local/kraken2_db_preparation/environment.yml b/modules/local/kraken2_db_preparation/environment.yml
@@ -0,0 +1,7 @@
+name: kraken2_db_preparation
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - conda-forge::sed=4.7
diff --git a/modules/local/kraken2_db_preparation.nf → modules/local/kraken2_db_preparation/main.nf b/modules/local/kraken2_db_preparation.nf → modules/local/kraken2_db_preparation/main.nf
@@ -2,16 +2,17 @@ process KRAKEN2_DB_PREPARATION {
     tag "${db.simpleName}"
     label 'process_low'
 
-    conda 'conda-forge::sed=4.7'
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :
-        'docker.io/biocontainers/biocontainers:v1.2.0_cv1' }"
+        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
+        'nf-core/ubuntu:20.04' }"
 
     input:
     path db
 
     output:
     tuple val("${db.simpleName}"), path("database"), emit: db
+    path "versions.yml"                            , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -22,5 +23,10 @@ process KRAKEN2_DB_PREPARATION {
     tar -xf "${db}" -C db_tmp
     mkdir database
     mv `find db_tmp/ -name "*.k2d"` database/
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        tar: \$(tar --version | sed -n 's/^tar (GNU tar) \$([0-9.]*\$).*/\$1/p')
+    END_VERSIONS
     """
 }
diff --git a/modules/local/medaka/environment.yml b/modules/local/medaka/environment.yml
@@ -0,0 +1,7 @@
+name: medaka
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - medaka=1.4.3-0
diff --git a/modules/local/medaka.nf → modules/local/medaka/main.nf b/modules/local/medaka.nf → modules/local/medaka/main.nf
@@ -2,7 +2,7 @@ process MEDAKA {
     tag "$meta.id"
     label 'process_high'
 
-    conda 'medaka=1.4.3-0'
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/medaka:1.4.3--py38h130def0_0' :
         'biocontainers/medaka:1.4.3--py38h130def0_0' }"

diff --git a/modules/local/nanopolish/environment.yml b/modules/local/nanopolish/environment.yml
@@ -0,0 +1,7 @@
+name: nanopolish
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::nanopolish=0.14.0
diff --git a/modules/local/nanopolish.nf → modules/local/nanopolish/main.nf b/modules/local/nanopolish.nf → modules/local/nanopolish/main.nf
@@ -2,7 +2,7 @@ process NANOPOLISH {
     tag "$meta.id"
     label 'process_high'
 
-    conda "bioconda::nanopolish=0.14.0"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/nanopolish:0.14.0--h773013f_3' :
         'biocontainers/nanopolish:0.14.0--h773013f_3' }"

diff --git a/modules/local/pycoqc/environment.yml b/modules/local/pycoqc/environment.yml
@@ -0,0 +1,7 @@
+name: pycoqc
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::pycoqc=2.5.2
diff --git a/modules/local/pycoqc.nf → modules/local/pycoqc/main.nf b/modules/local/pycoqc.nf → modules/local/pycoqc/main.nf
@@ -1,7 +1,7 @@
 process PYCOQC {
     label 'process_medium'
 
-    conda "bioconda::pycoqc=2.5.2"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/pycoqc:2.5.2--py_0' :
         'biocontainers/pycoqc:2.5.2--py_0' }"

diff --git a/modules/local/unicycler/environment.yml b/modules/local/unicycler/environment.yml
@@ -0,0 +1,7 @@
+name: unicycler
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - unicycler=0.4.8
diff --git a/modules/local/unicycler.nf → modules/local/unicycler/main.nf b/modules/local/unicycler.nf → modules/local/unicycler/main.nf
@@ -2,7 +2,7 @@ process UNICYCLER {
     tag "$meta.id"
     label 'process_high'
 
-    conda "bioconda::unicycler=0.4.8"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/unicycler:0.4.8--py38h8162308_3' :
         'biocontainers/unicycler:0.4.8--py38h8162308_3' }"

diff --git a/modules/nf-core/bakta/bakta/environment.yml b/modules/nf-core/bakta/bakta/environment.yml
diff --git a/modules/nf-core/bakta/bakta/main.nf b/modules/nf-core/bakta/bakta/main.nf
diff --git a/modules/nf-core/bakta/bakta/meta.yml b/modules/nf-core/bakta/bakta/meta.yml
diff --git a/modules/nf-core/bakta/bakta/tests/main.nf.test b/modules/nf-core/bakta/bakta/tests/main.nf.test