nf-core modules update all with prefix annotation

.github/workflows/ci.yml

@@ -26,6 +26,7 @@ jobs:
           - 'aligner'
           - 'annotation'
           - 'default'
+          - 'split_fastq'
           - 'gatk4_spark'
           - 'save_bam_mapped'
           - 'skip_markduplicates'

conf/modules.config

@@ -6,7 +6,8 @@
         ext.args            = Additional arguments appended to command in module.
         ext.args2           = Second set of arguments appended to command in module (multi-tool modules).
         ext.args3           = Third set of arguments appended to command in module (multi-tool modules).
-        ext.suffix          = File name ext.suffix output files.
+        ext.suffix          = File name ext.suffix output files. Not available for nf-core modules
+        ext.prefix          = File name ext.prefix output files.
 ----------------------------------------------------------------------------------------
 */
 
@@ -126,6 +127,8 @@ process {
         ext.args         = { meta.status == 1 ? '-K 100000000 -M -B 3' : '-K 100000000 -M' }
         ext.args2        = 'sort'
         publishDir       = [ enabled: false ]
+        ext.prefix       = { params.split_fastq > 1 ? "${meta.id}".concat(reads.get(0).name.findAll(/part_([0-9]+)?/).last().concat('.')) : "${meta.id}" }
+
     }
 
     withName: 'INDEX_MAPPING' {
@@ -141,7 +144,7 @@ process {
     }
 
     withName: 'SEQKIT_SPLIT2' {
-        ext.args         = "--by-size ${params.split_fastq}"
+        ext.args         = { "--by-size ${params.split_fastq}" }
         publishDir       = [ enabled: false ]
     }
 }
@@ -334,17 +337,17 @@ process {
 
     withName: 'ENSEMBLVEP' {
         ext.args          = '--everything --filter_common --per_gene --total_length --offline'
-        ext.container_tag = { "104.3.${params.genome}" }
+        container         = { "nfcore/vep:104.3.${params.genome}" }
         publishDir        = [ enabled: false ]
     }
 
     withName: 'SNPEFF' {
         ext.args          = '-nodownload -canon -v'
-        ext.container_tag = { "5.0.${params.genome}" }
+        container         = { "nfcore/snpeff:5.0.${params.genome}" }
         publishDir        = [ enabled: false ]
     }
 
-    withName: 'BGZIPTABIX_ANNOTATE' {
+    withName: 'ANNOTATION_BGZIPTABIX' {
         publishDir       = [
                 path: { "${params.outdir}/annotation/${meta.id}" },
                 enabled: true,
@@ -356,24 +359,24 @@ process {
 
 if ((params.tools) && (params.tools.contains('snpeff') || params.tools.contains('merge'))) {
     process {
-        withName: 'NFCORE_SAREK:SAREK:ANNOTATE:SNPEFF_ANNOTATE:BGZIPTABIX_ANNOTATE' {
-            ext.suffix = '_snpEff.ann.vcf'
+        withName: 'NFCORE_SAREK:SAREK:ANNOTATE:ANNOTATION_SNPEFF:ANNOTATION_BGZIPTABIX' {
+            ext.prefix = {"${meta.id}_snpEff.ann.vcf"}
         }
     }
 }
 
 if ((params.tools) && (params.tools.contains('vep'))) {
     process {
-        withName: 'NFCORE_SAREK:SAREK:ANNOTATE:ENSEMBLVEP_ANNOTATE:BGZIPTABIX_ANNOTATE' {
-            ext.suffix = '_VEP.ann.vcf'
+        withName: 'NFCORE_SAREK:SAREK:ANNOTATE:ANNOTATION_ENSEMBLVEP:ANNOTATION_BGZIPTABIX' {
+            ext.prefix = {"${meta.id}_VEP.ann.vcf"}
         }
     }
 }
 
 if ((params.tools) && (params.tools.contains('merge'))) {
     process {
-        withName: 'NFCORE_SAREK:SAREK:ANNOTATE:MERGE_ANNOTATE:BGZIPTABIX_ANNOTATE' {
-            ext.suffix = '_snpEff_VEP.ann.vcf'
+        withName: 'NFCORE_SAREK:SAREK:ANNOTATE:MERGE_ANNOTATE:ANNOTATION_BGZIPTABIX' {
+            ext.prefix = {"${meta.id}_snpEff_VEP.ann.vcf"}
         }
     }
 }

conf/test.config

@@ -55,7 +55,7 @@ profiles {
         params.skip_markduplicates = true
     }
     split_fastq {
-        params.split_fastq         = 2
+        params.split_fastq         = 1500
     }
     targeted {
         params.target_bed          = 'https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/target.bed'
@@ -104,4 +104,11 @@ process {
     withName:ENSEMBLVEP {
         maxForks = 1
     }
+    withName:SEQKIT_SPLIT2{
+        publishDir = [
+        path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
+        mode: 'copy',
+        saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
 }

modules.json

@@ -13,31 +13,31 @@
                 "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
             },
             "ensemblvep": {
-                "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
+                "git_sha": "3b366c7c6aac446c1a4ea7c2016092344633b2ec"
             },
             "fastqc": {
-                "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
+                "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961"
             },
             "freebayes": {
-                "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
+                "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961"
             },
             "gatk4/createsequencedictionary": {
                 "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
             },
             "manta/germline": {
-                "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
+                "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961"
             },
             "manta/somatic": {
-                "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
+                "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961"
             },
             "manta/tumoronly": {
-                "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
+                "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961"
             },
             "multiqc": {
                 "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
             },
             "samtools/faidx": {
-                "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
+                "git_sha": "e0aa89141ffecb5f54d230f7ea46de242b74e084"
             },
             "samtools/merge": {
                 "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
@@ -46,25 +46,25 @@
                 "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
             },
             "seqkit/split2": {
-                "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
+                "git_sha": "7006699ff8e4351e4c95d548de959d4222c7862a"
             },
             "snpeff": {
-                "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
+                "git_sha": "3b366c7c6aac446c1a4ea7c2016092344633b2ec"
             },
             "strelka/germline": {
-                "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
+                "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961"
             },
             "strelka/somatic": {
-                "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
+                "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961"
             },
             "tabix/bgziptabix": {
-                "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
+                "git_sha": "e22966ce74340cb671576143e5fdbbd71670cffa"
             },
             "tabix/tabix": {
                 "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
             },
             "trimgalore": {
-                "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
+                "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961"
             }
         }
     }

modules/local/bwa/mem/main.nf

@@ -19,8 +19,7 @@ process BWA_MEM {
     def split_cpus = Math.floor(task.cpus/2)
     def args = task.ext.args  ?: ''
     def args2 = task.ext.args2 ?: ''
-    def part = params.split_fastq > 1 ? reads.get(0).name.findAll(/part_([0-9]+)?/).last().concat('.') : ""
-    def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
+    def prefix = task.ext.prefix ?: "${meta.id}"
     def read_group = meta.read_group ? "-R ${meta.read_group}" : ""
     """
     INDEX=`find -L ./ -name "*.amb" | sed 's/.amb//'`

modules/local/bwamem2/mem/main.nf

@@ -19,8 +19,7 @@ process BWAMEM2_MEM {
     def split_cpus = Math.floor(task.cpus/2)
     def args       = task.ext.args  ?: ''
     def args2      = task.ext.args2 ?: ''
-    def part       = params.split_fastq > 1 ? reads.get(0).name.findAll(/part_([0-9]+)?/).last().concat('.') : ""
-    def prefix     = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
+    def prefix     = task.ext.prefix ?: "${meta.id}"
     def read_group = meta.read_group ? "-R ${meta.read_group}" : ""
     """
     INDEX=`find -L ./ -name "*.amb" | sed 's/.amb//'`