Update Genrich module input tuple and argument (nf-core#3720)

* Added treat & control lists inputs and SE modifier * Added treat & control lists inputs and SE modifier * Genrich: Added multiple reps and SE modifier * Genrich: Added multiple reps and SE modifier 2 * Genrich: simplified layout definition * Removing value channels * Line up commas * Align commas * Increase test -p to avoid empty file --------- Co-authored-by: Simon Pearce <[email protected]> Co-authored-by: Friederike Hanssen <[email protected]>
louperelo · Oct 18, 2023 · 53cb517 · 53cb517
1 parent e18a2de
commit 53cb517
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diff --git a/modules/nf-core/genrich/main.nf b/modules/nf-core/genrich/main.nf
@@ -8,54 +8,43 @@ process GENRICH {
         'biocontainers/genrich:0.6.1--h5bf99c6_1' }"
 
     input:
-    tuple val(meta), path(treatment_bam)
-    path  control_bam
+    tuple val(meta), path(treatment_bam), path(control_bam)
     path  blacklist_bed
-    val   save_pvalues
-    val   save_pileup
-    val   save_bed
-    val   save_duplicates
 
     output:
-    tuple val(meta), path("*narrowPeak")                     , emit: peaks
-    tuple val(meta), path("*pvalues.bedGraph"), optional:true, emit: bedgraph_pvalues
-    tuple val(meta), path("*pileup.bedGraph") , optional:true, emit: bedgraph_pileup
-    tuple val(meta), path("*intervals.bed")   , optional:true, emit: bed_intervals
-    tuple val(meta), path("*duplicates.txt")  , optional:true, emit: duplicates
-    path "versions.yml"                                      , emit: versions
+    tuple val(meta), path("*.narrowPeak")                     , emit: peak
+    path "versions.yml"                                       , emit: versions
+
+    tuple val(meta), path("*.pvalues.bedGraph"), optional:true, emit: bedgraph_pvalues
+    tuple val(meta), path("*.pileup.bedGraph") , optional:true, emit: bedgraph_pileup
+    tuple val(meta), path("*.intervals.bed")   , optional:true, emit: bed_intervals
+    tuple val(meta), path("*.duplicates.txt")  , optional:true, emit: duplicates
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
-    def control    = control_bam    ? "-c $control_bam"               : ''
-    def blacklist  = blacklist_bed  ? "-E $blacklist_bed"             : ""
-    def pvalues    = save_pvalues   ? "-f ${prefix}.pvalues.bedGraph" : ""
-    def pileup     = save_pileup    ? "-k ${prefix}.pileup.bedGraph"  : ""
-    def bed        = save_bed       ? "-b ${prefix}.intervals.bed"    : ""
-    def duplicates = ""
-    if (save_duplicates) {
-        if (args.contains('-r')) {
-            duplicates = "-R ${prefix}.duplicates.txt"
-        } else {
-            log.info '[Genrich] Duplicates can only be saved if they are filtered, defaulting to -r option (Remove PCR duplicates).'
-            duplicates = "-r -R ${prefix}.duplicates.txt"
-        }
+    def args       = task.ext.args   ?: ""
+    def prefix     = task.ext.prefix ?: "${meta.id}"
+    def treatment  = treatment_bam   ? "-t ${treatment_bam.join(',')}"   : ""
+    def control    = control_bam     ? "-c ${control_bam.join(',')}"     : ""
+    def blacklist  = blacklist_bed   ? "-E $blacklist_bed"               : ""
+
+    if (meta.single_end && (!args.contains("-y") && !args.contains("-w"))) {
+        log.info '[Genrich] Single-end data can only be analyzed if unpaired alignments are kept (-y or -w <int>), defaulting to -y option.'
+        args = "-y ${args}"
+    }
+    if (args.contains("-R") && !args.contains("-r")) {
+        log.info '[Genrich] Duplicates can only be saved if they are filtered out, defaulting to -r option (Remove PCR duplicates).'
+        args = "-r ${args}"
     }
     """
     Genrich \\
-        -t $treatment_bam \\
         $args \\
+        $treatment \\
         $control \\
         $blacklist \\
-        -o ${prefix}.narrowPeak \\
-        $pvalues \\
-        $pileup \\
-        $bed \\
-        $duplicates \\
-        $control
+        -o ${prefix}.narrowPeak
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/modules/nf-core/genrich/meta.yml b/modules/nf-core/genrich/meta.yml
@@ -23,11 +23,11 @@ input:
         e.g. [ id:'test', single_end:false ]
   - treatment_bam:
       type: file
-      description: Coordinate sorted BAM/SAM file from treatment sample
+      description: Coordinate sorted BAM/SAM file from treatment sample or list of BAM/SAM files from biological replicates
       pattern: "*.{bam,sam}"
   - control_bam:
       type: file
-      description: Coordinate sorted BAM/SAM file from control sample
+      description: Coordinate sorted BAM/SAM file from control sample or list of BAM/SAM files from control samples
       pattern: "*.{bam,sam}"
   - blacklist_bed:
       type: file
@@ -77,3 +77,4 @@ output:
       pattern: "*.{version.txt}"
 authors:
   - "@JoseEspinosa"
+  - "@samuelruizperez"
diff --git a/tests/modules/nf-core/genrich/main.nf b/tests/modules/nf-core/genrich/main.nf
@@ -4,76 +4,73 @@ nextflow.enable.dsl = 2
 
 include { GENRICH } from '../../../../modules/nf-core/genrich/main.nf'
 include { GENRICH as GENRICH_CTRL    } from '../../../../modules/nf-core/genrich/main.nf'
+include { GENRICH as GENRICH_SE      } from '../../../../modules/nf-core/genrich/main.nf'
 include { GENRICH as GENRICH_ALL     } from '../../../../modules/nf-core/genrich/main.nf'
 include { GENRICH as GENRICH_ATACSEQ } from '../../../../modules/nf-core/genrich/main.nf'
+include { GENRICH as GENRICH_LIST } from '../../../../modules/nf-core/genrich/main.nf'
 
 workflow test_genrich {
     input     = [ [ id:'test', single_end:false ], // meta map
-                  [ file( params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true) ]]
-    control   = [ ]
+                  [ file( params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true) ],
+                  [ ]]
     blacklist = [ ]
 
-    save_pvalues    = false
-    save_pileup     = false
-    save_bed        = false
-    save_duplicates = false
-
-    GENRICH ( input, control, blacklist, save_pvalues, save_pileup, save_bed, save_duplicates )
+    GENRICH ( input, blacklist )
 }
 
 workflow test_genrich_ctrl {
     input     = [ [ id:'test', single_end:false ], // meta map
-                  [ file( params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true) ]]
-    control   = [ file( params.test_data['homo_sapiens']['illumina']['test2_paired_end_name_sorted_bam'], checkIfExists: true) ]
+                  [ file( params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true) ],
+                  [ file( params.test_data['homo_sapiens']['illumina']['test2_paired_end_name_sorted_bam'], checkIfExists: true) ]]
     blacklist = [ ]
 
-    save_pvalues    = false
-    save_pileup     = false
-    save_bed        = false
-    save_duplicates = false
+    GENRICH_CTRL ( input, blacklist )
+}
+
+workflow test_genrich_se {
+    input     = [ [ id:'test', single_end:true ], // meta map
+                  [ file( params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true) ],
+                  [ file( params.test_data['homo_sapiens']['illumina']['test2_paired_end_name_sorted_bam'], checkIfExists: true) ]]
+    blacklist = [ ]
 
-    GENRICH_CTRL ( input, control, blacklist, save_pvalues, save_pileup, save_bed, save_duplicates )
+    GENRICH_SE ( input, blacklist )
 }
 
+
 workflow test_genrich_all_outputs {
     input     = [ [ id:'test', single_end:false ], // meta map
-                  [ file( params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true) ]]
-    control   = [ file( params.test_data['homo_sapiens']['illumina']['test2_paired_end_name_sorted_bam'], checkIfExists: true) ]
+                  [ file( params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true) ],
+                  [ file( params.test_data['homo_sapiens']['illumina']['test2_paired_end_name_sorted_bam'], checkIfExists: true) ]]
     blacklist = [ ]
 
-    save_pvalues    = true
-    save_pileup     = true
-    save_bed        = true
-    save_duplicates = true
-
-    GENRICH_ALL ( input, control, blacklist, save_pvalues, save_pileup, save_bed, save_duplicates )
+    GENRICH_ALL ( input, blacklist )
 }
 
 workflow test_genrich_blacklist {
     input     = [ [ id:'test', single_end:false ], // meta map
-                  [ file( params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true) ]]
-    control   = [ ]
+                  [ file( params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true) ],
+                  [ ]]
     blacklist = [ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)]
 
-    save_pvalues    = false
-    save_pileup     = false
-    save_bed        = false
-    save_duplicates = false
-
-    GENRICH ( input, control, blacklist, save_pvalues, save_pileup, save_bed, save_duplicates )
+    GENRICH ( input, blacklist )
 }
 
 workflow test_genrich_atacseq {
     input     = [ [ id:'test', single_end:false ], // meta map
-                  [ file( params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true) ]]
-    control   = [ ]
+                  [ file( params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true) ],
+                  [ ]]
     blacklist = [ ]
 
-    save_pvalues    = false
-    save_pileup     = false
-    save_bed        = false
-    save_duplicates = false
+    GENRICH_ATACSEQ ( input, blacklist )
+}
+
+workflow test_genrich_list {
+    input     = [ [ id:'test', single_end:false ], // meta map
+                  [ file( params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true),
+                    file( params.test_data['homo_sapiens']['illumina']['test2_paired_end_name_sorted_bam'], checkIfExists: true)],
+                  [ ]]
+    blacklist = [ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)]
 
-    GENRICH_ATACSEQ ( input, control, blacklist, save_pvalues, save_pileup, save_bed, save_duplicates )
+    GENRICH_LIST ( input, blacklist )
 }
 
diff --git a/tests/modules/nf-core/genrich/nextflow.config b/tests/modules/nf-core/genrich/nextflow.config
@@ -10,12 +10,27 @@ process {
         ext.args = '-p 0.9'
     }
 
+    withName: GENRICH_SE {
+        ext.args = '-p 0.9'
+    }
+
     withName: GENRICH_ALL {
-        ext.args = '-r -p 0.1'
+        ext.args = {
+            [
+                "-p 0.9",
+                "-k ${meta.id}.pileup.bedGraph",
+                "-f ${meta.id}.pvalues.bedGraph",
+                "-b ${meta.id}.intervals.bed",
+                "-R ${meta.id}.duplicates.txt"
+            ].join(' ').trim()
+        }
     }
 
     withName: GENRICH_ATACSEQ {
         ext.args = '-j -p 0.1'
     }
 
+    withName: GENRICH_LIST {
+        ext.args = '-p 0.1'
+    }
 }
diff --git a/tests/modules/nf-core/genrich/test.yml b/tests/modules/nf-core/genrich/test.yml
@@ -1,21 +1,32 @@
 - name: genrich test_genrich
-  command: nextflow run ./tests/modules/nf-core/genrich -entry test_genrich -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/genrich/nextflow.config
+  command: nextflow run ./tests/modules/nf-core/genrich -entry test_genrich -c ./tests/config/nextflow.config
   tags:
     - genrich
   files:
     - path: output/genrich/test.narrowPeak
       md5sum: 6afabdd3f691c7c84c66ff8a23984681
+    - path: output/genrich/versions.yml
 
 - name: genrich test_genrich_ctrl
-  command: nextflow run ./tests/modules/nf-core/genrich -entry test_genrich_ctrl -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/genrich/nextflow.config
+  command: nextflow run ./tests/modules/nf-core/genrich -entry test_genrich_ctrl -c ./tests/config/nextflow.config
   tags:
     - genrich
   files:
     - path: output/genrich/test.narrowPeak
       md5sum: 2fcc392360b317f5ebee88cdbc149e05
+    - path: output/genrich/versions.yml
+
+- name: genrich test_genrich_se
+  command: nextflow run ./tests/modules/nf-core/genrich -entry test_genrich_se -c ./tests/config/nextflow.config
+  tags:
+    - genrich
+  files:
+    - path: output/genrich/test.narrowPeak
+      md5sum: 1a835e303b090b5eea91b8e4f5cc1df6
+    - path: output/genrich/versions.yml
 
 - name: genrich test_genrich_all_outputs
-  command: nextflow run ./tests/modules/nf-core/genrich -entry test_genrich_all_outputs -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/genrich/nextflow.config
+  command: nextflow run ./tests/modules/nf-core/genrich -entry test_genrich_all_outputs -c ./tests/config/nextflow.config
   tags:
     - genrich
   files:
@@ -24,24 +35,36 @@
     - path: output/genrich/test.intervals.bed
       md5sum: 4bea65caa3f4043d703af4b57161112e
     - path: output/genrich/test.narrowPeak
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
+      md5sum: 82bc06c2e44e4d91152a6ac6557a2c6e
     - path: output/genrich/test.pileup.bedGraph
       md5sum: 03e53848de695b5794f32f15b2709203
     - path: output/genrich/test.pvalues.bedGraph
-      md5sum: b14feef34b6d2379a173a734ca963cde
+      md5sum: 21ad9731340e9bedc30c4d34f7db7751
+    - path: output/genrich/versions.yml
 
 - name: genrich test_genrich_blacklist
-  command: nextflow run ./tests/modules/nf-core/genrich -entry test_genrich_blacklist -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/genrich/nextflow.config
+  command: nextflow run ./tests/modules/nf-core/genrich -entry test_genrich_blacklist -c ./tests/config/nextflow.config
   tags:
     - genrich
   files:
     - path: output/genrich/test.narrowPeak
       md5sum: 6afabdd3f691c7c84c66ff8a23984681
+    - path: output/genrich/versions.yml
 
 - name: genrich test_genrich_atacseq
-  command: nextflow run ./tests/modules/nf-core/genrich -entry test_genrich_atacseq -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/genrich/nextflow.config
+  command: nextflow run ./tests/modules/nf-core/genrich -entry test_genrich_atacseq -c ./tests/config/nextflow.config
   tags:
     - genrich
   files:
     - path: output/genrich/test.narrowPeak
       md5sum: ddea556b820f8be3695ffdf6c6f70aff
+    - path: output/genrich/versions.yml
+
+- name: genrich test_genrich_list
+  command: nextflow run ./tests/modules/nf-core/genrich -entry test_genrich_list -c ./tests/config/nextflow.config
+  tags:
+    - genrich
+  files:
+    - path: output/genrich/test.narrowPeak
+      md5sum: f793e0ff59274e6364151a7cd4eeeafd
+    - path: output/genrich/versions.yml