Export versions and pass to MultiQC

Author: jfy133

conf/modules.config

@@ -60,7 +60,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/reference/${meta.id}/" },
             mode: params.publish_dir_mode,
-            pattern: 'bowtie2',
+            pattern: 'bowtie2/',
             enabled: params.save_reference
         ]
     }

subworkflows/local/reference_indexing.nf

@@ -13,18 +13,22 @@ workflow REFERENCE_INDEXING {
     fasta_mapperindexdir
 
     main:
+    ch_versions = Channel.empty()
 
     // TODO add WARN: if fasta.ext == csv && fai/dict/mapperindexdir supplied, then latter will be ignored with preference for info in csv!
 
     if ( fasta_fai && fasta_dict && fasta_mapperindexdir ) {
         // TODO: if all are supplied
     } else if ( fasta.extension == 'csv' | fasta.extension == 'tsv' ) {
         ch_reference_for_mapping = REFERENCE_INDEXING_MULTI ( fasta ).reference
+        ch_versions = ch_versions.mix( REFERENCE_INDEXING_MULTI.out.versions )
     } else {
         ch_reference_for_mapping = REFERENCE_INDEXING_SINGLE ( fasta, fasta_fai, fasta_dict, fasta_mapperindexdir ).reference
+        ch_versions = ch_versions.mix( REFERENCE_INDEXING_SINGLE.out.versions )
     }
 
     emit:
     reference = ch_reference_for_mapping // [ meta, fasta, fai, dict, mapindex ]
+    versions  = ch_versions
 
 }

subworkflows/local/reference_indexing_single.nf

@@ -19,6 +19,8 @@ workflow REFERENCE_INDEXING_SINGLE {
 
     main:
 
+    ch_versions = Channel.empty()
+
     def fasta_ext = grab_ungzipped_extension(fasta)
     def clean_name = fasta.name.toString() - fasta_ext
 
@@ -29,20 +31,23 @@ workflow REFERENCE_INDEXING_SINGLE {
         ch_gz_ref = Channel.fromPath(fasta).map{[[], it]}
         GUNZIP ( ch_gz_ref )
         ch_ungz_ref = GUNZIP.out.gunzip.map{[[id: clean_name], it[1] ]}
+        ch_versions = ch_versions.mix( GUNZIP.out.versions )
     } else {
         ch_ungz_ref = Channel.fromPath(fasta).map{[[id: clean_name], it ]}
     }
 
     // Generate FAI if not supplied, and if supplied generate meta ID
     if ( !fasta_fai ) {
         ch_fasta_fai = SAMTOOLS_FAIDX ( ch_ungz_ref ).fai.map{[ [id: clean_name - '.fai'], it[1] ] }
+        ch_versions = ch_versions.mix( SAMTOOLS_FAIDX.out.versions )
     } else {
         ch_fasta_fai = Channel.fromPath(fasta_fai).map{[[id: clean_name], it ]}
     }
 
     // Generate DICT if not supplied, and if supplied generate meta
     if ( !fasta_dict ) {
         ch_fasta_dict = PICARD_CREATESEQUENCEDICTIONARY ( ch_ungz_ref ).reference_dict.map{[ [id: clean_name - '.fai'], it[1] ] }
+        ch_versions = ch_versions.mix( PICARD_CREATESEQUENCEDICTIONARY.out.versions )
     } else {
         ch_fasta_dict = Channel.fromPath(ch_fasta_dict).map{[[id: clean_name], it ]}
     }
@@ -52,6 +57,7 @@ workflow REFERENCE_INDEXING_SINGLE {
 
         if ( !fasta_mapperindexdir ) {
             ch_fasta_mapperindexdir = BWA_INDEX ( ch_ungz_ref ).index
+            ch_versions = ch_versions.mix( BWA_INDEX.out.versions )
         } else {
             ch_fasta_mapperindexdir = Channel.fromPath(fasta_mapperindexdir).map{[[id: clean_name], it ]}
         }
@@ -60,6 +66,7 @@ workflow REFERENCE_INDEXING_SINGLE {
 
         if ( !fasta_mapperindexdir ) {
             ch_fasta_mapperindexdir = BOWTIE2_BUILD ( ch_ungz_ref ).index
+            ch_versions = ch_versions.mix( BOWTIE2_BUILD.out.versions )
         } else {
             ch_fasta_mapperindexdir = Channel.fromPath(fasta_mapperindexdir).map{[[id: clean_name], it ]}
         }
@@ -75,6 +82,7 @@ workflow REFERENCE_INDEXING_SINGLE {
 
     emit:
     reference = ch_reference_for_mapping // [ meta, fasta, fai, dict, mapindex ]
+    versions  = ch_versions
 
 }
 

workflows/eager.nf

@@ -89,6 +89,7 @@ workflow EAGER {
     //
 
     REFERENCE_INDEXING ( fasta, fasta_fai, fasta_dict, fasta_mapperindexdir )
+    ch_versions = ch_versions.mix( REFERENCE_INDEXING.out.versions )
 
     //
     // MODULE: Run FastQC