remove HISAT2 process references and params pseudo_aligner

nf-core · May 15, 2024 · 725e74d · 725e74d
1 parent 759a486
commit 725e74d
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Showing 3 changed files with 3 additions and 13 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -39,7 +39,7 @@ process {
         ext.args2 = '--no-same-owner'
     }
 
-    withName: 'UNTAR_.*|STAR_GENOMEGENERATE|STAR_GENOMEGENERATE_IGENOMES|HISAT2_BUILD' {
+    withName: 'UNTAR_.*|STAR_GENOMEGENERATE|STAR_GENOMEGENERATE_IGENOMES' {
         publishDir = [
             path: { "${params.outdir}/genome/index" },
             mode: params.publish_dir_mode,
@@ -56,14 +56,6 @@ process {
         ]
     }
 
-    withName: 'HISAT2_EXTRACTSPLICESITES' {
-        publishDir = [
-            path: { "${params.outdir}/genome/index" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
-        ]
-    }
-
     withName: 'SALMON_INDEX' {
         ext.args   = { [
                 params.gencode ? '--gencode' : '',
@@ -84,7 +76,7 @@ process {
         ]
     }
 
-    withName: 'CAT_ADDITIONAL_FASTA|PREPROCESS_TRANSCRIPTS_FASTA_GENCODE' {
+    withName: 'CUSTOM_CATADDITIONALFASTA|PREPROCESS_TRANSCRIPTS_FASTA_GENCODE' {
         publishDir = [
             path: { "${params.outdir}/genome" },
             mode: params.publish_dir_mode,

diff --git a/main.nf b/main.nf
@@ -73,7 +73,6 @@ workflow NFCORE_RIBOSEQ {
         params.sortmerna_index,
         params.gencode,
         params.aligner,
-        params.pseudo_aligner,
         params.skip_gtf_filter,
         params.skip_bbsplit,
         ! params.remove_ribo_rna,

diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/local/prepare_genome/main.nf
@@ -43,8 +43,7 @@ workflow PREPARE_GENOME {
     bbsplit_index            // directory: /path/to/rsem/index/
     sortmerna_index          // directory: /path/to/sortmerna/index/
     gencode                  //   boolean: whether the genome is from GENCODE
-    aligner                  //    string: Specifies the alignment algorithm to use - available options are 'star_salmon', 'star_rsem' and 'hisat2'
-    pseudo_aligner           //    string: Specifies the pseudo aligner to use - available options are 'salmon'. Runs in addition to '--aligner'
+    aligner                  //    string: Specifies the alignment algorithm to use - available options are 'star'
     skip_gtf_filter          //   boolean: Skip filtering of GTF for valid scaffolds and/ or transcript IDs
     skip_bbsplit             //   boolean: Skip BBSplit for removal of non-reference genome reads
     skip_sortmerna           //   boolean: Skip sortmerna for removal of non-reference genome reads