Add stub star align genomegenerate (#1948)

* correct md5sum for updated star/samtools

* merge changes in align test.yml

* update md5sum for star genomegenerate

* update md5sum for star align

modules/star/align/main.nf

@@ -70,4 +70,28 @@ process STAR_ALIGN {
         gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//')
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}Xd.out.bam
+    touch ${prefix}.Log.final.out
+    touch ${prefix}.Log.out
+    touch ${prefix}.Log.progress.out
+    touch ${prefix}.sortedByCoord.out.bam
+    touch ${prefix}.toTranscriptome.out.bam
+    touch ${prefix}.Aligned.unsort.out.bam
+    touch ${prefix}.unmapped_1.fastq.gz
+    touch ${prefix}.unmapped_2.fastq.gz
+    touch ${prefix}.tab
+    touch ${prefix}.Chimeric.out.junction
+    touch ${prefix}.out.sam
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        star: \$(STAR --version | sed -e "s/STAR_//g")
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+        gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//')
+    END_VERSIONS
+    """
 }

modules/star/genomegenerate/main.nf

@@ -65,4 +65,32 @@ process STAR_GENOMEGENERATE {
         END_VERSIONS
         """
     }
+
+    stub:
+    """
+    mkdir star
+    touch star/Genome
+    touch star/Log.out
+    touch star/SA
+    touch star/SAindex
+    touch star/chrLength.txt
+    touch star/chrName.txt
+    touch star/chrNameLength.txt
+    touch star/chrStart.txt
+    touch star/exonGeTrInfo.tab
+    touch star/exonInfo.tab
+    touch star/geneInfo.tab
+    touch star/genomeParameters.txt
+    touch star/sjdbInfo.txt
+    touch star/sjdbList.fromGTF.out.tab
+    touch star/sjdbList.out.tab
+    touch star/transcriptInfo.tab
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        star: \$(STAR --version | sed -e "s/STAR_//g")
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+        gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//')
+    END_VERSIONS
+    """
 }

tests/modules/star/align/test.yml

@@ -175,3 +175,19 @@
     - path: output/star/test.Log.out
     - path: output/star/test.Log.progress.out
     - path: output/star/test.SJ.out.tab
+
+- name: star align test_star_alignment_single_end stub
+  command: nextflow run ./tests/modules/star/align -entry test_star_alignment_single_end -c ./tests/config/nextflow.config -c ./tests/modules/star/align/nextflow.config -stub-run
+  tags:
+    - star/align
+    - star
+  files:
+    - path: output/star/test.Aligned.unsort.out.bam
+    - path: output/star/test.Log.final.out
+    - path: output/star/test.Log.out
+    - path: output/star/test.Log.progress.out
+    - path: output/star/test.Chimeric.out.junction
+    - path: output/star/test.unmapped_1.fastq.gz
+    - path: output/star/test.unmapped_2.fastq.gz
+    - path: output/star/test.tab
+    - path: output/star/test.out.sam

tests/modules/star/genomegenerate/test.yml

@@ -35,3 +35,26 @@
       md5sum: 9e4f991abbbfeb3935a2bb21b9e258f1
     - path: output/star/star/transcriptInfo.tab
       md5sum: 0c3a5adb49d15e5feff81db8e29f2e36
+
+- name: star genomegenerate test_star_genomegenerate stub
+  command: nextflow run ./tests/modules/star/genomegenerate -entry test_star_genomegenerate -c ./tests/config/nextflow.config -c ./tests/modules/star/genomegenerate/nextflow.config -stub-run
+  tags:
+    - star
+    - star/genomegenerate
+  files:
+    - path: output/star/star/Genome
+    - path: output/star/star/Log.out
+    - path: output/star/star/SA
+    - path: output/star/star/SAindex
+    - path: output/star/star/chrLength.txt
+    - path: output/star/star/chrName.txt
+    - path: output/star/star/chrNameLength.txt
+    - path: output/star/star/chrStart.txt
+    - path: output/star/star/exonGeTrInfo.tab
+    - path: output/star/star/exonInfo.tab
+    - path: output/star/star/geneInfo.tab
+    - path: output/star/star/genomeParameters.txt
+    - path: output/star/star/sjdbInfo.txt
+    - path: output/star/star/sjdbList.fromGTF.out.tab
+    - path: output/star/star/sjdbList.out.tab
+    - path: output/star/star/transcriptInfo.tab