Add stubs to every process to allow stub runs

.markdownlint.yml

@@ -0,0 +1,14 @@
+# Markdownlint configuration file
+default: true
+line-length: false
+ul-indent:
+    indent: 4
+no-duplicate-header:
+    siblings_only: true
+no-inline-html:
+    allowed_elements:
+        - img
+        - p
+        - kbd
+        - details
+        - summary

.nf-core.yml

@@ -0,0 +1,10 @@
+lint:
+    files_exist:
+    - assets/nf-core-ARETE_logo.png
+    - docs/images/nf-core-ARETE_logo.png
+    files_unchanged:
+    - assets/email_template.html
+    - assets/multiqc_config.yaml
+    nextflow_config:
+    - params.input
+    - manifest.name

modules/local/blast_databases.nf

@@ -16,6 +16,10 @@ process GET_VFDB{
     """
     curl http://www.mgc.ac.cn/VFs/Down/VFDB_setB_pro.fas.gz --output VFDB_setB_pro.fas.gz
     """
+    stub:
+    """
+    touch VFDB_setB_pro.fas.gz
+    """
 }
 
 process GET_BACMET{
@@ -26,4 +30,8 @@ process GET_BACMET{
     """
     curl http://bacmet.biomedicine.gu.se/download/BacMet2_predicted_database.fasta.gz --output BacMet2_predicted_database.fasta.gz
     """
+    stub:
+    """
+    touch BacMet2_predicted_database.fasta.gz
+    """
 }

modules/local/get_minikraken.nf

@@ -17,4 +17,8 @@ process KRAKEN2_DB {
     mkdir -p k2_standard_8gb_20201202
     tar xvf k2_standard_8gb_20201202.tar.gz -C k2_standard_8gb_20201202
     """
+    stub:
+    """
+    mkdir -p k2_standard_8gb_20201202
+    """
 }

modules/local/mobsuite.nf

@@ -37,6 +37,12 @@ process MOB_RECON {
     mob_recon --version > ${software}.version.txt
     """
     //--database_directory $mob_db  \\
+    stub:
+    def software = getSoftwareName(task.process)
+    """
+    mkdir ${meta.id}_mob_recon
+    mob_recon --version > ${software}.version.txt
+    """
 }
 
 // MOB_INIT also exists but seems to be unneeded.

modules/local/rgi.nf

@@ -53,4 +53,11 @@ process RGI {
 
     echo \$(rgi main --version 2>&1) > ${software}.version.txt
     """
+    stub:
+    def software = getSoftwareName(task.process)
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    """
+    touch ${prefix}_rgi.txt
+    echo \$(rgi main --version 2>&1) > ${software}.version.txt
+    """
 }

modules/nf-core/modules/blast/blastn/main.nf

@@ -41,4 +41,13 @@ process BLAST_BLASTN {
         ${getSoftwareName(task.process)}: \$(blastn -version 2>&1 | sed 's/^.*blastn: //; s/ .*\$//')
     END_VERSIONS
     """
+    stub:
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    """
+    touch ${prefix}.blastn.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(blastn -version 2>&1 | sed 's/^.*blastn: //; s/ .*\$//')
+    END_VERSIONS
+    """
 }

modules/nf-core/modules/blast/makeblastdb/main.nf

@@ -37,4 +37,12 @@ process BLAST_MAKEBLASTDB {
         ${getSoftwareName(task.process)}: \$(blastn -version 2>&1 | sed 's/^.*blastn: //; s/ .*\$//')
     END_VERSIONS
     """
+    stub:
+    """
+    mkdir blast_db
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(blastn -version 2>&1 | sed 's/^.*blastn: //; s/ .*\$//')
+    END_VERSIONS
+    """
 }

modules/nf-core/modules/checkm/lineagewf/main.nf

@@ -48,4 +48,14 @@ process CHECKM_LINEAGEWF {
         checkm: \$( checkm 2>&1 | grep '...:::' | sed 's/.*CheckM v//;s/ .*//' )
     END_VERSIONS
     """
+    stub:
+    prefix   = task.ext.prefix ?: "${meta.id}"
+    """
+    mkdir ${prefix}
+    touch ${prefix}.tsv
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        checkm: \$( checkm 2>&1 | grep '...:::' | sed 's/.*CheckM v//;s/ .*//' )
+    END_VERSIONS
+    """
 }

modules/nf-core/modules/diamond/blastx/main.nf

@@ -47,4 +47,13 @@ process DIAMOND_BLASTX {
         ${getSoftwareName(task.process)}: \$(diamond --version 2>&1 | tail -n 1 | sed 's/^diamond version //')
     END_VERSIONS
     """
+    stub:
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    """
+    touch ${prefix}_${label}.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(diamond --version 2>&1 | tail -n 1 | sed 's/^diamond version //')
+    END_VERSIONS
+    """
 }

modules/nf-core/modules/diamond/makedb/main.nf

@@ -41,4 +41,13 @@ process DIAMOND_MAKEDB {
         ${getSoftwareName(task.process)}: \$(diamond --version 2>&1 | tail -n 1 | sed 's/^diamond version //')
     END_VERSIONS
     """
+
+    stub:
+    """
+    touch ${fasta}.dmnd
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(diamond --version 2>&1 | tail -n 1 | sed 's/^diamond version //')
+    END_VERSIONS
+    """
 }

modules/nf-core/modules/fastp/main.nf

@@ -79,4 +79,16 @@ process FASTP {
         END_VERSIONS
         """
     }
+    stub:
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    """
+    touch ${prefix}.trim.fastq.gz
+    touch ${prefix}.trim.fastp.html
+    touch ${prefix}.trim.fastp.json
+    touch ${prefix}.trim.fastp.log
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(fastp --version 2>&1 | sed -e "s/fastp //g")
+    END_VERSIONS
+    """
 }

modules/nf-core/modules/fastqc/main.nf

@@ -45,4 +45,13 @@ process FASTQC {
         fastqc --version | sed -e "s/FastQC v//g" > ${software}.version.txt
         """
     }
+
+    stub:
+    def software = getSoftwareName(task.process)
+    def prefix   = "${meta.id}.${run_name}"
+    """
+    touch ${prefix}.fastqcstub.html
+    touch ${prefix}.fastqcstub.zip
+    fastqc --version | sed -e "s/FastQC v//g" > ${software}.version.txt
+    """
 }

modules/nf-core/modules/iqtree/main.nf

@@ -43,4 +43,13 @@ process IQTREE {
         ${getSoftwareName(task.process)}: \$(echo \$(iqtree -version 2>&1) | sed 's/^IQ-TREE multicore version //;s/ .*//')
     END_VERSIONS
     """
+
+    stub:
+    """
+    touch faketree.treefile
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(echo \$(iqtree -version 2>&1) | sed 's/^IQ-TREE multicore version //;s/ .*//')
+    END_VERSIONS
+    """
 }

modules/nf-core/modules/kraken2/kraken2/main.nf

@@ -52,4 +52,17 @@ process KRAKEN2_KRAKEN2 {
         pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
     END_VERSIONS
     """
+
+    stub:
+    def prefix       = options.suffix  ? "${meta.id}${options.suffix}"  : "${meta.id}"
+    """
+    touch ${prefix}.classified.fastq.gz
+    touch ${prefix}.unclassified.fastq.gz
+    touch ${prefix}.kraken2.report.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(echo \$(kraken2 --version 2>&1) | sed 's/^.*Kraken version //; s/ .*\$//')
+        pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
+    END_VERSIONS
+    """
 }

modules/nf-core/modules/multiqc/main.nf

@@ -32,4 +32,13 @@ process MULTIQC {
     multiqc -f $options.args .
     multiqc --version | sed -e "s/multiqc, version //g" > ${software}.version.txt
     """
+
+    stub:
+    def software = getSoftwareName(task.process)
+    """
+    touch stub_multiqc_report.html
+    mkdir multiqc_stub_data
+    mkdir multiqc_stub_reports
+    multiqc --version | sed -e "s/multiqc, version //g" > ${software}.version.txt
+    """
 }

modules/nf-core/modules/prokka/main.nf

@@ -57,4 +57,26 @@ process PROKKA {
         ${getSoftwareName(task.process)}: \$(echo \$(prokka --version 2>&1) | sed 's/^.*prokka //')
     END_VERSIONS
     """
+
+    stub:
+    prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    """
+    mkdir ${prefix}
+    touch ${prefix}/${prefix}_stub.err
+    touch ${prefix}/${prefix}_stub.ffn
+    touch ${prefix}/${prefix}_stub.faa
+    touch ${prefix}/${prefix}_stub.gbk
+    touch ${prefix}/${prefix}_stub.fna
+    touch ${prefix}/${prefix}_stub.fsa
+    touch ${prefix}/${prefix}_stub.gff
+    touch ${prefix}/${prefix}_stub.log
+    touch ${prefix}/${prefix}_stub.sqn
+    touch ${prefix}/${prefix}_stub.tbl
+    touch ${prefix}/${prefix}_stub.tsv
+    touch ${prefix}/${prefix}_stub.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(echo \$(prokka --version 2>&1) | sed 's/^.*prokka //')
+    END_VERSIONS
+    """
 }

modules/nf-core/modules/quast/main.nf

@@ -48,4 +48,16 @@ process QUAST {
         ${getSoftwareName(task.process)}: \$(quast.py --version 2>&1 | sed 's/^.*QUAST v//; s/ .*\$//')
     END_VERSIONS
     """
+
+    stub:
+    def software  = getSoftwareName(task.process)
+    prefix        = options.suffix ?: software
+    """
+    mkdir ${prefix}
+    touch ${prefix}_quast_stub.tsv
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(quast.py --version 2>&1 | sed 's/^.*QUAST v//; s/ .*\$//')
+    END_VERSIONS
+    """
 }

modules/nf-core/modules/roary/main.nf

@@ -40,4 +40,14 @@ process ROARY {
         ${getSoftwareName(task.process)}: \$( roary --version )
     END_VERSIONS
     """
+
+    stub:
+    """
+    mkdir results
+    touch results/roary_stub.aln
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$( roary --version )
+    END_VERSIONS
+    """
 }

modules/nf-core/modules/snpsites/main.nf

@@ -42,4 +42,14 @@ process SNPSITES {
         ${getSoftwareName(task.process)}: \$(snp-sites -V 2>&1 | sed 's/snp-sites //')
     END_VERSIONS
     """
+    stub:
+    """
+    touch snpsites_stub.fas
+    echo acgt > snpsites_stub.sites.txt
+    CONSTANT_SITES=\$(cat snpsites_stub.sites.txt)
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(snp-sites -V 2>&1 | sed 's/snp-sites //')
+    END_VERSIONS
+    """
 }

modules/nf-core/modules/unicycler/main.nf

@@ -56,4 +56,16 @@ process UNICYCLER {
         ${getSoftwareName(task.process)}: \$(echo \$(unicycler --version 2>&1) | sed 's/^.*Unicycler v//; s/ .*\$//')
     END_VERSIONS
     """
+    stub:
+
+    def prefix      = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    """
+    touch ${prefix}_stub.scaffolds.fa
+    touch ${prefix}_stub.assembly.gfa
+    touch ${prefix}_stub.unicylcer.log
+        cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(echo \$(unicycler --version 2>&1) | sed 's/^.*Unicycler v//; s/ .*\$//')
+    END_VERSIONS
+    """
 }