Merge pull request #475 from nf-core/nftest-implementation

Author: edmundmiller

.gitignore

@@ -7,3 +7,5 @@ testing/
 testing*
 *.pyc
 null/
+
+.nf-test*

docs/output.md

@@ -321,7 +321,6 @@ Once installed, open IGV, go to `File > Open Session` and select the `igv_sessio
 - `genome/`
   - A number of genome-specific files are generated by the pipeline in order to aid in the filtering of the data, and because they are required by standard tools such as BEDTools. These can be found in this directory along with the genome fasta file which is required by IGV. If using a genome from AWS iGenomes and if it exists a `README.txt` file containing information about the annotation version will also be saved in this directory.
 - `genome/index/`
-
   - `bwa/`: Directory containing BWA indices.
   - `bowtie2/`: Directory containing BOWTIE2 indices.
   - `chromap/`: Directory containing Chromap indices.

modules/local/bam_remove_orphans.nf

@@ -43,4 +43,15 @@ process BAM_REMOVE_ORPHANS {
         END_VERSIONS
         """
     }
+
+    stub:
+    prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.bam
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+    END_VERSIONS
+    """
 }

modules/local/bamtools_filter.nf

@@ -40,4 +40,16 @@ process BAMTOOLS_FILTER {
         bamtools: \$(echo \$(bamtools --version 2>&1) | sed 's/^.*bamtools //; s/Part .*\$//')
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.bam
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+        bamtools: \$(echo \$(bamtools --version 2>&1) | sed 's/^.*bamtools //; s/Part .*\$//')
+    END_VERSIONS
+    """
 }

modules/local/bedtools_genomecov.nf

@@ -40,4 +40,16 @@ process BEDTOOLS_GENOMECOV {
         bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.bedGraph
+    touch ${prefix}.scale_factor.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
+    END_VERSIONS
+    """
 }

modules/local/frip_score.nf

@@ -31,4 +31,16 @@ process FRIP_SCORE {
         samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.FRiP.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+    END_VERSIONS
+    """
 }

modules/local/multiqc.nf

@@ -71,4 +71,16 @@ process MULTIQC {
         multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
     END_VERSIONS
     """
+
+    stub:
+    """
+    mkdir -p multiqc_data
+    touch multiqc_report.html
+    touch multiqc_data/multiqc.log
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
+    END_VERSIONS
+    """
 }

modules/local/multiqc_custom_phantompeakqualtools.nf

@@ -33,4 +33,17 @@ process MULTIQC_CUSTOM_PHANTOMPEAKQUALTOOLS {
         r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//')
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.spp_nsc_mqc.tsv
+    touch ${prefix}.spp_rsc_mqc.tsv
+    touch ${prefix}.spp_correlation_mqc.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//')
+    END_VERSIONS
+    """
 }

nf-test.config

@@ -19,6 +19,6 @@ config {
 
     // load the necessary plugins
     plugins {
-        load "[email protected].3"
+        load "[email protected].5"
     }
 }