"change_name" process and configuration of output file name

conf/modules.config

@@ -131,7 +131,7 @@ process {
 
     withName: '.*:CONVERT_STATS:SAMTOOLS_CRAM' {
         beforeScript = { "export REF_PATH=spoof"}
-        ext.prefix = { "${fasta.baseName}.${meta.datatype}.${meta.id}" }
+        ext.prefix = { "${input.baseName}" }
         ext.args   = '--output-fmt cram --write-index'
     }
 
@@ -158,28 +158,32 @@ process {
         ext.args   = { (meta.datatype == "pacbio" ? "-y pbccs " : "") + "-O bam" }
     }
 
-    withName: '.*:CONVERT_STATS:SAMTOOLS_.*|BGZIP_BEDGRAPH|CHANGE_NAME' {
+    withName: '.*:CONVERT_STATS:SAMTOOLS_.*|BGZIP_BEDGRAPH' {
         beforeScript = { "export REF_PATH=spoof" }
         publishDir = [
             path: { "${params.outdir}/read_mapping/${meta.datatype}${meta.merged ? '/merged' : ''}" },
             mode: params.publish_dir_mode,
-            // Only publish BAM/CRAM from SAMTOOLS_REHEADER if params.header is true, else from: CHANGE_NAME and SAMTOOLS_CRAM
+            // Only publish BAM/CRAM from SAMTOOLS_REHEADER if params.header is true, else from: SAMTOOLS_INDEX (BAM) and SAMTOOLS_CRAM (CRAM)
             saveAs: { filename ->
-                filename == 'versions.yml' || ((task.process =~ /CHANGE_NAME|SAMTOOLS_CRAM/) && params.header) ? null : filename
+                filename == 'versions.yml'
+                || ((task.process == 'CHANGE_NAME') || (task.process == 'SAMTOOLS_CRAM' && !file.name.endsWith('.cram'))
+                    && params.header)
+                || ((task.process =~ /SAMTOOLS_CRAM/) && filename.endsWith(".bam"))
+                ? null : filename
             }
         ]
     }
 
     withName: 'BLOBTK_DEPTH' {
-        ext.prefix = { "${meta.fasta}.${meta.datatype}.${meta.id}" }
+        ext.prefix = { "${bam.baseName}" }
     }
 
     withName: 'BGZIP_BEDGRAPH' {
         ext.prefix = { "${input.baseName}" }
     }
 
     withName: 'CHANGE_NAME' {
-        ext.prefix = { "${meta.fasta}.${meta.datatype}.${meta.id}" }
+        ext.prefix = { "${fasta.baseName}.${meta.datatype}.${meta.id}" }
     }
 
     withName: FASTQC {

modules.json

@@ -58,7 +58,8 @@
                     "samtools/index": {
                         "branch": "master",
                         "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/samtools/index/samtools-index.diff"
                     },
                     "samtools/merge": {
                         "branch": "master",

modules/local/change_name.nf

@@ -4,6 +4,7 @@ process CHANGE_NAME {
 
     input:
     tuple val(meta), path(file)
+    tuple val(meta2), path(fasta)
 
     output:
     tuple val(meta), path("*.${file.extension}"), emit: file

subworkflows/local/convert_stats.nf

@@ -32,12 +32,6 @@ workflow CONVERT_STATS {
     // Split outfmt parameter into a list
     def outfmt_options = params.outfmt.split(',').collect { it.trim() }
 
-    // Reserve fasta base name for prefix of CHANGE_NAME and BLOBTK_DEPTH
-    bam
-    .combine( fasta )
-    .map{ meta, bam, meta1, fasta -> [ meta +[fasta:fasta.baseName], bam]}
-    .set { bam }
-
     // (Optionally) Compress the quality scores of Illumina and PacBio CCS alignments
     if ( params.compression == "crumble" ) {
         bam
@@ -53,30 +47,33 @@ workflow CONVERT_STATS {
 
         CRUMBLE.out.bam
         | mix( crumble_selector.no_crumble )
-        | map { meta, bam -> [meta, bam, []] }
-        | set { ch_bams_for_conversion }
+        | set { ch_bams_for_renaming }
 
     } else {
-        bam
-        | map { meta, bam -> [meta, bam, []] }
-        | set { ch_bams_for_conversion }
+        ch_bams_for_renaming = bam
     }
 
 
+    // Change name of BAM files to final name for publishing
+    CHANGE_NAME ( ch_bams_for_renaming, fasta )
+
+    CHANGE_NAME.out.file
+    | map { meta, bam -> [meta, bam, []] }
+    | set { ch_renamed_bams }
+
+
     // (Optionally) convert to CRAM if it's specified in outfmt
     ch_cram = Channel.empty()
     ch_crai = Channel.empty()
 
     if ("cram" in outfmt_options) {
-        SAMTOOLS_CRAM ( ch_bams_for_conversion, fasta, [] )
+        SAMTOOLS_CRAM ( ch_renamed_bams, fasta, [] )
         ch_versions = ch_versions.mix( SAMTOOLS_CRAM.out.versions.first() )
 
         // Combine CRAM and CRAI into one channel
         ch_cram = SAMTOOLS_CRAM.out.cram
         ch_crai = SAMTOOLS_CRAM.out.crai
-        ch_data_for_stats = ch_cram.join( ch_crai )
-    } else {
-        ch_data_for_stats = ch_bams_for_conversion
+        ch_for_stats = ch_cram.join( ch_crai )
     }
 
 
@@ -85,23 +82,21 @@ workflow CONVERT_STATS {
     ch_bai = Channel.empty()
 
     if ("bam" in outfmt_options) {
-        ch_bams_to_index = ch_bams_for_conversion.map{ it -> [it[0], it[1]]}
-        // Change name of BAM files to final name for publishing
-        ch_bam = CHANGE_NAME ( ch_bams_to_index ).file
-
         // Reindex BAM
-        SAMTOOLS_INDEX ( ch_bam )
+        SAMTOOLS_INDEX ( CHANGE_NAME.out.file )
         ch_versions = ch_versions.mix( SAMTOOLS_INDEX.out.versions.first() )
 
         // Set the BAM and BAI channels for emission
+        ch_bam = CHANGE_NAME.out.file
         ch_bai = SAMTOOLS_INDEX.out.bai.mix(SAMTOOLS_INDEX.out.csi)
 
-        // If using BAM for stats, use the reindexed BAM
-        if ( !("cram" in outfmt_options) ) {
-            ch_data_for_stats = ch_bam.join ( SAMTOOLS_INDEX.out.bai )
+        if ( !('cram' in outfmt_options) ) {
+            ch_for_stats = ch_bam.join( ch_bai )
         }
+
     }
 
+
     // Optionally insert params.header information to bams
     if ( params.header ) {
         ch_bam = SAMTOOLS_REHEADER_BAM ( ch_bam, header.first() ).bam
@@ -112,25 +107,22 @@ workflow CONVERT_STATS {
 
 
     // Calculate read depth
-    BLOBTK_DEPTH ( ch_bams_for_conversion )
+    BLOBTK_DEPTH ( ch_renamed_bams )
     ch_versions = ch_versions.mix( BLOBTK_DEPTH.out.versions.first() )
 
     BGZIP_BEDGRAPH ( BLOBTK_DEPTH.out.bedgraph )
     ch_versions = ch_versions.mix( BGZIP_BEDGRAPH.out.versions.first() )
 
-
     // Calculate statistics
-    SAMTOOLS_STATS ( ch_data_for_stats, fasta )
+    SAMTOOLS_STATS (ch_for_stats, [[], []] )
     ch_versions = ch_versions.mix( SAMTOOLS_STATS.out.versions.first() )
 
-
     // Calculate statistics based on flag values
-    SAMTOOLS_FLAGSTAT ( ch_data_for_stats )
+    SAMTOOLS_FLAGSTAT ( ch_for_stats )
     ch_versions = ch_versions.mix( SAMTOOLS_FLAGSTAT.out.versions.first() )
 
-
     // Calculate index statistics
-    SAMTOOLS_IDXSTATS ( ch_data_for_stats )
+    SAMTOOLS_IDXSTATS ( ch_for_stats )
     ch_versions = ch_versions.mix( SAMTOOLS_IDXSTATS.out.versions.first() )