fix: separates contrast and contrastsheet params #196

CCBR · Mar 1, 2024 · 105dd26 · 105dd26
1 parent 0d8dc36
commit 105dd26
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Showing 6 changed files with 16 additions and 6 deletions.
diff --git a/conf/full_mm10.config b/conf/full_mm10.config
@@ -5,7 +5,8 @@ params {
     genome = 'mm10'
     outdir = "results/full_mm10"
     input = "${projectDir}/assets/samplesheet_full_mm10.csv"
-    contrasts = "${projectDir}/assets/contrasts_full_mm10.yml"
+    contrasts = 'true'
+    contrastsheet = "${projectDir}/assets/contrasts_full_mm10.yml"
     sicer {
         species = "mm10" // supported species https://github.com/zanglab/SICER2/blob/master/sicer/lib/GenomeData.py
     }

diff --git a/conf/test_human.config b/conf/test_human.config
@@ -5,7 +5,7 @@ params {
     genome = 'hg38'
     outdir = "results/human"
     input = "assets/samplesheet_human.csv"
-    contrasts = null //'assets/contrasts_human.yml'
+    contrasts = false //'assets/contrasts_human.yml'
     //read_length = 50
     sicer.species = "${params.genome}" // supported species https://github.com/zanglab/SICER2/blob/master/sicer/lib/GenomeData.py
 

diff --git a/conf/test_mm10.config b/conf/test_mm10.config
@@ -5,7 +5,8 @@ params {
     genome = 'mm10'
     outdir = "results/test_mm10"
     input = "${projectDir}/assets/samplesheet_test_mm10.csv"
-    contrasts = "${projectDir}/assets/contrasts_test_mm10.yml"
+    contrasts = 'true'
+    contrastsheet = "${projectDir}/assets/contrasts_test_mm10.yml"
     read_length = 50
     sicer.species = "mm10" // supported species https://github.com/zanglab/SICER2/blob/master/sicer/lib/GenomeData.py
 

diff --git a/main.nf b/main.nf
@@ -36,6 +36,9 @@ include { PHANTOM_PEAKS
           PPQT_PROCESS
           MULTIQC                  } from "./modules/local/qc.nf"
 
+
+contrastsheet = params.contrastsheet ?: "/assets/contrast_test.ymls"
+
 workflow.onComplete {
     if (!workflow.stubRun && !workflow.commandLine.contains('-preview')) {
         def message = Utils.spooker(workflow)
@@ -64,7 +67,7 @@ workflow {
 }
 
 workflow CHIPSEQ {
-    INPUT_CHECK(file(params.input, checkIfExists: true), params.seq_center, file(params.contrasts, checkIfExists: true))
+    INPUT_CHECK(file(params.input, checkIfExists: true), params.seq_center, file(contrastsheet))
 
     INPUT_CHECK.out.reads.set { raw_fastqs }
     raw_fastqs | CUTADAPT

diff --git a/nextflow.config b/nextflow.config
@@ -2,11 +2,14 @@ nextflow.enable.dsl = 2
 
 params {
     input = null
-    contrasts = null
+    contrasts = false
     seq_center = null
     read_length = null
     genome = null
 
+    // manifest for contrasts
+    contrastsheet = null
+
     // custom genome options
     genome_fasta = null
     genes_gtf   = null

diff --git a/subworkflows/local/input_check.nf b/subworkflows/local/input_check.nf
@@ -19,6 +19,8 @@ workflow INPUT_CHECK {
             .map { create_fastq_channel(it, seq_center) }
             .set { reads }
 
+        // Run check on the contrast manifest
+        contrasts=Channel.empty()
         if (params.contrasts) {
             CHECK_CONTRASTS(valid_csv, contrastsheet)
                 .csv
@@ -33,7 +35,7 @@ workflow INPUT_CHECK {
         }
 
     emit:
-        reads                                     // channel: [ val(meta), [ reads ] ]
+        reads                               = reads      // channel: [ val(meta), [ reads ] ]
         csv                                 = valid_csv
         contrasts                           = contrasts
         versions                            = SAMPLESHEET_CHECK.out.versions // channel: [ versions.yml ]