bismark: remove underscores from process names (#303)

* sanitize process names

no underscores allowed

* remove underscores from process names

software/bismark/genomepreparation/main.nf

@@ -4,7 +4,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions'
 params.options = [:]
 options        = initOptions(params.options)
 
-process BISMARK_GENOME_PREPARATION {
+process BISMARK_GENOMEPREPARATION {
     tag "$fasta"
     label 'process_high'
     publishDir "${params.outdir}",

software/bismark/genomepreparation/meta.yml

@@ -1,4 +1,4 @@
-name: bismark_genome_preparation
+name: bismark_genomepreparation
 description: |
     Converts a specified reference genome into two different bisulfite
     converted versions and indexes them for alignments.

software/bismark/methylationextractor/main.nf

@@ -4,7 +4,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions'
 params.options = [:]
 options        = initOptions(params.options)
 
-process BISMARK_METHYLATION_EXTRACTOR {
+process BISMARK_METHYLATIONEXTRACTOR {
     tag "$meta.id"
     label 'process_high'
     publishDir "${params.outdir}",

software/bismark/methylationextractor/meta.yml

@@ -1,4 +1,4 @@
-name: bismark_methylation_extractor
+name: bismark_methylationextractor
 description: Extracts methylation information for individual cytosines from alignments.
 keywords:
     - bismark

tests/config/pytest_software.yml

@@ -60,21 +60,21 @@ bedtools_sort:
 
 bismark_align:
   - software/bismark/align/**
-  - software/bismark/genome_preparation/**
+  - software/bismark/genomepreparation/**
   - tests/software/bismark/align/**
 
 bismark_deduplicate:
   - software/bismark/deduplicate/**
   - tests/software/bismark/deduplicate/**
 
-bismark_genome_preparation:
+bismark_genomepreparation:
-  - software/bismark/genome_preparation/**
+  - software/bismark/genomepreparation/**
-  - tests/software/bismark/genome_preparation/**
+  - tests/software/bismark/genomepreparation/**
 
-bismark_methylation_extractor:
+bismark_methylationextractor:
-  - software/bismark/methylation_extractor/**
+  - software/bismark/methylationextractor/**
-  - software/bismark/genome_preparation/**
+  - software/bismark/genomepreparation/**
-  - tests/software/bismark/methylation_extractor/**
+  - tests/software/bismark/methylationextractor/**
 
 
 blast_blastn:
@@ -82,18 +82,18 @@ blast_blastn:
   - tests/software/blast/blastn/**
 
 bismark_report:
-  - software/bismark/genome_preparation/**
+  - software/bismark/genomepreparation/**
   - software/bismark/align/**
   - software/bismark/deduplicate/**
-  - software/bismark/methylation_extractor/**
+  - software/bismark/methylationextractor/**
   - software/bismark/report/**
   - tests/software/bismark/report/**
 
 bismark_summary:
-  - software/bismark/genome_preparation/**
+  - software/bismark/genomepreparation/**
   - software/bismark/align/**
   - software/bismark/deduplicate/**
-  - software/bismark/methylation_extractor/**
+  - software/bismark/methylationextractor/**
   - software/bismark/summary/**
   - tests/software/bismark/summary/**
 

tests/software/bismark/align/main.nf

@@ -2,7 +2,7 @@
 
 nextflow.enable.dsl = 2
 
-include { BISMARK_GENOME_PREPARATION } from '../../../../software/bismark/genome_preparation/main.nf' addParams( options: [:] )
+include { BISMARK_GENOMEPREPARATION } from '../../../../software/bismark/genomepreparation/main.nf' addParams( options: [:] )
 include { BISMARK_ALIGN as BISMARK_ALIGN_SE } from '../../../../software/bismark/align/main.nf'  addParams( options: [ publish_dir:'test_single_end' ] )
 include { BISMARK_ALIGN as BISMARK_ALIGN_PE } from '../../../../software/bismark/align/main.nf'  addParams( options: [ publish_dir:'test_paired_end' ] )
 
@@ -16,10 +16,10 @@ workflow test_bismark_align_single_end {
               [ file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_methylated_1.fastq.gz", checkIfExists: true) ] ]
 
 
-    BISMARK_GENOME_PREPARATION ( file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true) )
+    BISMARK_GENOMEPREPARATION ( file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true) )
     BISMARK_ALIGN_SE (
         input,
-        BISMARK_GENOME_PREPARATION.out.index
+        BISMARK_GENOMEPREPARATION.out.index
     )
 }
 
@@ -34,9 +34,9 @@ workflow test_bismark_align_paired_end {
                 file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_methylated_2.fastq.gz", checkIfExists: true) ] ]
 
 
-    BISMARK_GENOME_PREPARATION ( file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true) )
+    BISMARK_GENOMEPREPARATION ( file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true) )
     BISMARK_ALIGN_PE (
         input,
-        BISMARK_GENOME_PREPARATION.out.index
+        BISMARK_GENOMEPREPARATION.out.index
     )
 }

tests/software/bismark/genome_preparation/main.nf

@@ -1,10 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BISMARK_GENOME_PREPARATION } from '../../../../software/bismark/genome_preparation/main.nf' addParams( options: [:] )
-
-workflow test_bismark_genome_preparation {
-
-    BISMARK_GENOME_PREPARATION ( file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true) )
-}

tests/software/bismark/genomepreparation/main.nf

@@ -0,0 +1,10 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BISMARK_GENOMEPREPARATION } from '../../../../software/bismark/genomepreparation/main.nf' addParams( options: [:] )
+
+workflow test_bismark_genomepreparation {
+
+    BISMARK_GENOMEPREPARATION ( file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true) )
+}

tests/software/bismark/genomepreparation/test.yml

@@ -1,8 +1,8 @@
-- name: Run bismark_genome_preparation test workflow
+- name: Run bismark_genomepreparation test workflow
-  command: nextflow run ./tests/software/bismark/genome_preparation -entry test_bismark_genome_preparation -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/bismark/genomepreparation -entry test_bismark_genomepreparation -c tests/config/nextflow.config
   tags:
     - bismark
-    - bismark_genome_preparation
+    - bismark_genomepreparation
   files:
     - path: ./output/bismark/BismarkIndex/test_genome.fasta
       md5sum: 6e9fe4042a72f2345f644f239272b7e6

tests/software/bismark/methylation_extractor/main.nf

@@ -1,20 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BISMARK_GENOME_PREPARATION    } from '../../../../software/bismark/genome_preparation/main.nf' addParams( options: [:] )
-include { BISMARK_METHYLATION_EXTRACTOR } from '../../../../software/bismark/methylation_extractor/main.nf' addParams( options: [:] )
-
-workflow test_bismark_methylation_extractor {
-
-    def input = []
-    input = [ [ id:'test', single_end:false ], // meta map
-              [ file("${launchDir}/tests/data/genomics/sarscov2/bam/test_methylated_paired_end.bam", checkIfExists: true) ] ]
-
-    BISMARK_GENOME_PREPARATION ( file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true) )
-
-    BISMARK_METHYLATION_EXTRACTOR (
-        input,
-        BISMARK_GENOME_PREPARATION.out.index
-    )
-}

tests/software/bismark/methylationextractor/main.nf

@@ -0,0 +1,20 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BISMARK_GENOMEPREPARATION    } from '../../../../software/bismark/genomepreparation/main.nf' addParams( options: [:] )
+include { BISMARK_METHYLATIONEXTRACTOR } from '../../../../software/bismark/methylationextractor/main.nf' addParams( options: [:] )
+
+workflow test_bismark_methylationextractor {
+
+    def input = []
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file("${launchDir}/tests/data/genomics/sarscov2/bam/test_methylated_paired_end.bam", checkIfExists: true) ] ]
+
+    BISMARK_GENOMEPREPARATION ( file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true) )
+
+    BISMARK_METHYLATIONEXTRACTOR (
+        input,
+        BISMARK_GENOMEPREPARATION.out.index
+    )
+}

tests/software/bismark/methylationextractor/test.yml

@@ -1,8 +1,8 @@
 - name: Run bismark methylation extractor test workflow
-  command: nextflow run ./tests/software/bismark/methylation_extractor -entry test_bismark_methylation_extractor -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/bismark/methylationextractor -entry test_bismark_methylationextractor -c tests/config/nextflow.config
   tags:
     - bismark
-    - bismark_methylation_extractor
+    - bismark_methylationextractor
   files:
     - path: output/bismark/CHG_OB_test_methylated_paired_end.txt.gz
     - path: output/bismark/CHG_OT_test_methylated_paired_end.txt.gz

tests/software/bismark/report/main.nf

@@ -2,10 +2,10 @@
 
 nextflow.enable.dsl = 2
 
-include { BISMARK_GENOME_PREPARATION    } from '../../../../software/bismark/genome_preparation/main.nf' addParams( options: [:] )
+include { BISMARK_GENOMEPREPARATION    } from '../../../../software/bismark/genomepreparation/main.nf' addParams( options: [:] )
 include { BISMARK_ALIGN                 } from '../../../../software/bismark/align/main.nf' addParams( options: [:] )
 include { BISMARK_DEDUPLICATE           } from '../../../../software/bismark/deduplicate/main.nf' addParams( options: [:] )
-include { BISMARK_METHYLATION_EXTRACTOR } from '../../../../software/bismark/methylation_extractor/main.nf' addParams( options: [:] )
+include { BISMARK_METHYLATIONEXTRACTOR } from '../../../../software/bismark/methylationextractor/main.nf' addParams( options: [:] )
 include { BISMARK_REPORT                } from '../../../../software/bismark/report/main.nf' addParams( options: [:] )
 
 workflow test_bismark_report {
@@ -15,15 +15,15 @@ workflow test_bismark_report {
               [ file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_methylated_1.fastq.gz", checkIfExists: true),
                 file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_methylated_2.fastq.gz", checkIfExists: true) ] ]
 
-    BISMARK_GENOME_PREPARATION ( file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true) )
+    BISMARK_GENOMEPREPARATION ( file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true) )
-    BISMARK_ALIGN ( input, BISMARK_GENOME_PREPARATION.out.index )
+    BISMARK_ALIGN ( input, BISMARK_GENOMEPREPARATION.out.index )
     BISMARK_DEDUPLICATE ( BISMARK_ALIGN.out.bam )
-    BISMARK_METHYLATION_EXTRACTOR ( BISMARK_DEDUPLICATE.out.bam, BISMARK_GENOME_PREPARATION.out.index )
+    BISMARK_METHYLATIONEXTRACTOR ( BISMARK_DEDUPLICATE.out.bam, BISMARK_GENOMEPREPARATION.out.index )
 
     BISMARK_REPORT (
         BISMARK_ALIGN.out.report
             .join(BISMARK_DEDUPLICATE.out.report)
-            .join(BISMARK_METHYLATION_EXTRACTOR.out.report)
+            .join(BISMARK_METHYLATIONEXTRACTOR.out.report)
-            .join(BISMARK_METHYLATION_EXTRACTOR.out.mbias)
+            .join(BISMARK_METHYLATIONEXTRACTOR.out.mbias)
     )
 }

tests/software/bismark/summary/main.nf

@@ -2,10 +2,10 @@
 
 nextflow.enable.dsl = 2
 
-include { BISMARK_GENOME_PREPARATION    } from '../../../../software/bismark/genome_preparation/main.nf' addParams( options: [:] )
+include { BISMARK_GENOMEPREPARATION    } from '../../../../software/bismark/genomepreparation/main.nf' addParams( options: [:] )
 include { BISMARK_ALIGN                 } from '../../../../software/bismark/align/main.nf' addParams( options: [:] )
 include { BISMARK_DEDUPLICATE           } from '../../../../software/bismark/deduplicate/main.nf' addParams( options: [:] )
-include { BISMARK_METHYLATION_EXTRACTOR } from '../../../../software/bismark/methylation_extractor/main.nf' addParams( options: [:] )
+include { BISMARK_METHYLATIONEXTRACTOR } from '../../../../software/bismark/methylationextractor/main.nf' addParams( options: [:] )
 include { BISMARK_SUMMARY               } from '../../../../software/bismark/summary/main.nf' addParams( options: [:] )
 
 workflow test_bismark_summary {
@@ -15,16 +15,16 @@ workflow test_bismark_summary {
               [ file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_methylated_1.fastq.gz", checkIfExists: true),
                 file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_methylated_2.fastq.gz", checkIfExists: true) ] ]
 
-    BISMARK_GENOME_PREPARATION ( file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true) )
+    BISMARK_GENOMEPREPARATION ( file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true) )
-    BISMARK_ALIGN ( input, BISMARK_GENOME_PREPARATION.out.index )
+    BISMARK_ALIGN ( input, BISMARK_GENOMEPREPARATION.out.index )
     BISMARK_DEDUPLICATE ( BISMARK_ALIGN.out.bam )
-    BISMARK_METHYLATION_EXTRACTOR ( BISMARK_DEDUPLICATE.out.bam, BISMARK_GENOME_PREPARATION.out.index )
+    BISMARK_METHYLATIONEXTRACTOR ( BISMARK_DEDUPLICATE.out.bam, BISMARK_GENOMEPREPARATION.out.index )
 
     BISMARK_SUMMARY (
         BISMARK_ALIGN.out.bam.collect{ meta, bam -> bam },
         BISMARK_ALIGN.out.report.collect{ meta, report -> report },
         BISMARK_DEDUPLICATE.out.report.collect{ meta, bam -> bam },
-        BISMARK_METHYLATION_EXTRACTOR.out.report.collect{ meta, report -> report },
+        BISMARK_METHYLATIONEXTRACTOR.out.report.collect{ meta, report -> report },
-        BISMARK_METHYLATION_EXTRACTOR.out.mbias.collect{ meta, mbias -> mbias }
+        BISMARK_METHYLATIONEXTRACTOR.out.mbias.collect{ meta, mbias -> mbias }
     )
 }