Contribute and install fastq_subsample_fq_salmon subworkflow from nf-core/modules

Author: drpatelh

conf/modules.config

@@ -182,7 +182,7 @@ process {
         ]
     }
 
-    withName: '.*:FASTQ_SAMPLE_INFER_STRANDEDNESS_FQ_SALMON:SALMON_QUANT' {
+    withName: '.*:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT' {
         ext.args   = '--skipQuant'
         publishDir = [
             path: { "${params.outdir}/sample_fastq/salmon" },

modules.json

@@ -34,7 +34,7 @@
                     "fq/subsample": {
                         "branch": "master",
                         "git_sha": "ad462aa294faf9a8c42688a08daf81a580594f70",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules", "fastq_subsample_fq_salmon"]
                     },
                     "gffread": {
                         "branch": "master",
@@ -134,7 +134,7 @@
                     "salmon/quant": {
                         "branch": "master",
                         "git_sha": "94b06f1683ddf893cf06525f6e7f0573ad8fbf83",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules", "fastq_subsample_fq_salmon"]
                     },
                     "samtools/flagstat": {
                         "branch": "master",
@@ -267,6 +267,11 @@
                         "branch": "master",
                         "git_sha": "b51a69e30973c71950225c817ad07a3337d22c40",
                         "installed_by": ["subworkflows"]
+                    },
+                    "fastq_subsample_fq_salmon": {
+                        "branch": "master",
+                        "git_sha": "0098bc93f6219c6194f443f0feb089ba83717384",
+                        "installed_by": ["subworkflows"]
                     }
                 }
             }

subworkflows/local/fastq_sample_infer_strandedness_fq_salmon.nf renamed to subworkflows/nf-core/fastq_subsample_fq_salmon/main.nf

@@ -113,7 +113,6 @@ include { ALIGN_STAR     } from '../subworkflows/local/align_star'
 include { QUANTIFY_RSEM  } from '../subworkflows/local/quantify_rsem'
 include { QUANTIFY_SALMON as QUANTIFY_STAR_SALMON } from '../subworkflows/local/quantify_salmon'
 include { QUANTIFY_SALMON as QUANTIFY_SALMON      } from '../subworkflows/local/quantify_salmon'
-include { FASTQ_SAMPLE_INFER_STRANDEDNESS_FQ_SALMON } from '../subworkflows/local/fastq_sample_infer_strandedness_fq_salmon.nf'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -137,6 +136,7 @@ include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoft
 //
 // SUBWORKFLOW: Consisting entirely of nf-core/modules
 //
+include { FASTQ_SUBSAMPLE_FQ_SALMON                 } from '../subworkflows/nf-core/fastq_subsample_fq_salmon/main'
 include { FASTQ_FASTQC_UMITOOLS_TRIMGALORE          } from '../subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main'
 include { FASTQ_ALIGN_HISAT2                        } from '../subworkflows/nf-core/fastq_align_hisat2/main'
 include { BAM_SORT_STATS_SAMTOOLS                   } from '../subworkflows/nf-core/bam_sort_stats_samtools/main'
@@ -231,15 +231,15 @@ workflow RNASEQ {
     //
     // SUBWORKFLOW: Sub-sample FastQ files and pseudo-align with Salmon to auto-infer strandedness
     //
-    FASTQ_SAMPLE_INFER_STRANDEDNESS_FQ_SALMON (
+    FASTQ_SUBSAMPLE_FQ_SALMON (
         ch_strand_fastq.auto_strand,
         PREPARE_GENOME.out.salmon_index,
         ch_dummy_file,
         PREPARE_GENOME.out.gtf
     )
-    ch_versions = ch_versions.mix(FASTQ_SAMPLE_INFER_STRANDEDNESS_FQ_SALMON.out.versions)
+    ch_versions = ch_versions.mix(FASTQ_SUBSAMPLE_FQ_SALMON.out.versions)
 
-    FASTQ_SAMPLE_INFER_STRANDEDNESS_FQ_SALMON
+    FASTQ_SUBSAMPLE_FQ_SALMON
         .out
         .json_info
         .join(ch_strand_fastq.auto_strand)