seacr | local testing implimented

software/seacr/callpeak/main.nf

@@ -36,6 +36,6 @@ process SEACR_CALLPEAK {
         $options.args \\
         $prefix
 
-    echo 1.3' > ${software}.version.txt
+    echo 1.3 > ${software}.version.txt
     """
 }

tests/software/seacr/main.nf

@@ -0,0 +1,20 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SEACR_CALLPEAK } from '../../../software/seacr/callpeak/main.nf' addParams( options: [ args:'norm stringent' ] )
+
+workflow test_seacr_callpeak {
+
+    def input = []
+    input = [[ id:'test_1'],
+              file("${launchDir}/tests/data/bedgraph/K27me3_1_to_chr20.bedgraph", checkIfExists: true),
+              file("${launchDir}/tests/data/bedgraph/IgG_1_to_chr20.bedgraph", checkIfExists: true) ]
+
+    SEACR_CALLPEAK ( input )
+}
+
+// For local testing
+workflow {
+    test_seacr_callpeak()
+}

tests/software/seacr/test.yml

@@ -0,0 +1,44 @@
+- name: Run samtools call peak test workflow
+  command: nextflow run ./tests/software/samtools/ -profile docker -entry test_samtools_flagstat -c tests/config/nextflow.config
+  tags:
+    - samtools
+    - samtools_flagstat
+  files:
+    - path: output/samtools/test.paired_end.sorted.bam.flagstat
+      md5sum: 80590621c74f5ee43ada20d010a3837f
+
+- name: Run samtools idxstats test workflow
+  command: nextflow run ./tests/software/samtools/ -profile docker -entry test_samtools_idxstats -c tests/config/nextflow.config
+  tags:
+    - samtools
+    - samtools_idxstats
+  files:
+    - path: output/samtools/test.paired_end.sorted.bam.idxstats
+      md5sum: 3bee8b7d55e412da2b3816c5a18d60d5
+
+- name: Run samtools index test workflow
+  command: nextflow run ./tests/software/samtools/ -profile docker -entry test_samtools_index -c tests/config/nextflow.config
+  tags:
+    - samtools
+    - samtools_index
+  files:
+    - path: output/samtools/test.paired_end.sorted.bam.bai
+      md5sum: 67338c2995eae82c849830ca55aa7bd1
+
+- name: Run samtools sort test workflow
+  command: nextflow run ./tests/software/samtools/ -profile docker -entry test_samtools_sort -c tests/config/nextflow.config
+  tags:
+    - samtools
+    - samtools_sort
+  files:
+    - path: output/samtools/test.bam
+      md5sum: a41bfadacd2eeef1d31e05c135cc4f4e
+
+- name: Run samtools stats test workflow
+  command: nextflow run ./tests/software/samtools/ -profile docker -entry test_samtools_stats -c tests/config/nextflow.config
+  tags:
+    - samtools
+    - samtools_stats
+  files:
+    - path: output/samtools/test.paired_end.sorted.bam.stats
+      md5sum: 06c183864d6e47ab89b0650cae831a93