diff --git a/modules/nf-core/blobtk/plot/main.nf b/modules/nf-core/blobtk/plot/main.nf index b18d8948a67c..f1ccdcdb6259 100644 --- a/modules/nf-core/blobtk/plot/main.nf +++ b/modules/nf-core/blobtk/plot/main.nf @@ -36,8 +36,8 @@ process BLOBTK_PLOT { error "BLOBTK_PLOT can't use both local_path and online_path, use `[]` as input for the unused channel." } - resource = online_path ?: local_path - prefix = task.ext.prefix ?: "${meta.id}" + def resource = online_path ?: local_path + prefix = task.ext.prefix ?: "${meta.id}" """ blobtk plot \\ @@ -52,7 +52,7 @@ process BLOBTK_PLOT { """ stub: - def prefix = task.ext.prefix ?: "${meta.id}" + prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}.png diff --git a/modules/nf-core/cellranger/count/main.nf b/modules/nf-core/cellranger/count/main.nf index 6f9bedf7126a..6b2058de72f0 100644 --- a/modules/nf-core/cellranger/count/main.nf +++ b/modules/nf-core/cellranger/count/main.nf @@ -20,7 +20,7 @@ process CELLRANGER_COUNT { if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { error "CELLRANGER_COUNT module does not support Conda. Please use Docker / Singularity / Podman instead." } - args = task.ext.args ?: '' + def args = task.ext.args ?: '' prefix = task.ext.prefix ?: "${meta.id}" template "cellranger_count.py" @@ -29,7 +29,7 @@ process CELLRANGER_COUNT { if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { error "CELLRANGER_COUNT module does not support Conda. Please use Docker / Singularity / Podman instead." } - def prefix = task.ext.prefix ?: "${meta.id}" + prefix = task.ext.prefix ?: "${meta.id}" """ mkdir -p "${prefix}/outs/" echo "$prefix" > ${prefix}/outs/fake_file.txt diff --git a/modules/nf-core/cellrangerarc/mkref/main.nf b/modules/nf-core/cellrangerarc/mkref/main.nf index 13b5d2f13bbf..f10287528c15 100644 --- a/modules/nf-core/cellrangerarc/mkref/main.nf +++ b/modules/nf-core/cellrangerarc/mkref/main.nf @@ -27,7 +27,7 @@ process CELLRANGERARC_MKREF { def fast_name = fasta.name def gtf_name = gtf.name def motifs_name = motifs.name - def reference_config = reference_config.name + def reference_config_name = reference_config.name def args = task.ext.args ?: '' if ( !reference_name ){ @@ -46,7 +46,7 @@ process CELLRANGERARC_MKREF { gtf = "${gtf_name}" motifs = "${motifs_name}" add = "${args}" - reference_config = "${reference_config}" + reference_config = "${reference_config_name}" if ( reference_config == "[]" ): diff --git a/modules/nf-core/chewbbaca/createschema/main.nf b/modules/nf-core/chewbbaca/createschema/main.nf index 90ca4ae45326..93600c1f1c39 100644 --- a/modules/nf-core/chewbbaca/createschema/main.nf +++ b/modules/nf-core/chewbbaca/createschema/main.nf @@ -25,8 +25,8 @@ process CHEWBBACA_CREATESCHEMA { def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def schema = "--n ${prefix}" - def prodigal_tf = prodigal_tf ? "--ptf ${prodigal_tf}" : "" - def cds = cds ? "--cds ${cds}" : "" + def prodigal_tf_opt = prodigal_tf ? "--ptf ${prodigal_tf}" : "" + def cds_opt = cds ? "--cds ${cds}" : "" """ find ./input_genomes/ -name "*.gz" | sed 's/.gz//' | xargs -I {} bash -c 'gzip -cdf {}.gz > {}' @@ -37,8 +37,8 @@ process CHEWBBACA_CREATESCHEMA { -o results \\ $schema \\ $args \\ - $prodigal_tf \\ - $cds \\ + $prodigal_tf_opt \\ + $cds_opt \\ --cpu $task.cpus cat <<-END_VERSIONS > versions.yml diff --git a/modules/nf-core/cnvnator/cnvnator/main.nf b/modules/nf-core/cnvnator/cnvnator/main.nf index 09b48e3baaef..f3d8ce7b2a68 100644 --- a/modules/nf-core/cnvnator/cnvnator/main.nf +++ b/modules/nf-core/cnvnator/cnvnator/main.nf @@ -50,10 +50,10 @@ process CNVNATOR_CNVNATOR { def args = task.ext.args ?: '' prefix = task.ext.prefix ?: bam ? "${meta.id}" : "${meta2.id}" output_meta = bam ? meta : meta2 - def calls_cmd = args.contains("-call") ? "touch ${prefix}.tab" : '' + def calls_cmd_opt = args.contains("-call") ? "touch ${prefix}.tab" : '' """ touch ${prefix}.root - $calls_cmd + $calls_cmd_opt cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/crumble/main.nf b/modules/nf-core/crumble/main.nf index 7eee3d5e0d3a..42a6a9481caa 100644 --- a/modules/nf-core/crumble/main.nf +++ b/modules/nf-core/crumble/main.nf @@ -30,7 +30,7 @@ process CRUMBLE { args.contains("-O cram") ? "cram" : "bam" def bedin = keepbed ? "-R ${keepbed}" : "" - def bedout = bedout ? "-b ${prefix}.out.bed" : "" + def bedout_opt = bedout ? "-b ${prefix}.out.bed" : "" if ("$input" == "${prefix}.${extension}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" def CRUMBLE_VERSION = '0.9.1' //WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. @@ -38,7 +38,7 @@ process CRUMBLE { crumble \\ $args \\ $bedin \\ - $bedout \\ + $bedout_opt \\ $input \\ ${prefix}.${extension} @@ -55,13 +55,13 @@ process CRUMBLE { args.contains("-O bam") ? "bam" : args.contains("-O cram") ? "cram" : "bam" - def bedout = bedout ? "touch ${prefix}.out.bed" : '' + def bedout_opt = bedout ? "touch ${prefix}.out.bed" : '' if ("$input" == "${prefix}.${extension}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" def CRUMBLE_VERSION = '0.9.1' //WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. """ touch ${prefix}.${extension} - $bedout + $bedout_opt cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/crumble/tests/main.nf.test b/modules/nf-core/crumble/tests/main.nf.test index ee520a4a00bf..a6d37f6c719f 100644 --- a/modules/nf-core/crumble/tests/main.nf.test +++ b/modules/nf-core/crumble/tests/main.nf.test @@ -31,7 +31,7 @@ nextflow_process { { assert process.success }, { assert snapshot( process.out.bam, - bam(process.out.cram[0][1]).getHeaderMD5(), + file(process.out.cram[0][1]).name, process.out.sam, process.out.bed, process.out.versions @@ -62,7 +62,7 @@ nextflow_process { { assert process.success }, { assert snapshot( process.out.bam, - bam(process.out.cram[0][1]).getHeaderMD5(), + file(process.out.cram[0][1]).name, process.out.sam, file(process.out.bed[0][1]).name, // empty process.out.versions diff --git a/modules/nf-core/crumble/tests/main.nf.test.snap b/modules/nf-core/crumble/tests/main.nf.test.snap index 8e4f8327b405..a6003029c49b 100644 --- a/modules/nf-core/crumble/tests/main.nf.test.snap +++ b/modules/nf-core/crumble/tests/main.nf.test.snap @@ -63,14 +63,14 @@ "test-crumble": { "content": [ [ - + ], - "12375c4b3bcdf1fc3d246a1238e37d7c", + "test.cram", [ - + ], [ - + ], [ "versions.yml:md5,42f81b0ca409a32457bf2e2017dcf8da" @@ -85,11 +85,11 @@ "test-crumble-bedout": { "content": [ [ - + ], - "36e5cf603a948d5a1217d86242cba41a", + "test.cram", [ - + ], "test.out.bed", [ diff --git a/modules/nf-core/diann/main.nf b/modules/nf-core/diann/main.nf index 1453401fdb88..2e6ca252d933 100644 --- a/modules/nf-core/diann/main.nf +++ b/modules/nf-core/diann/main.nf @@ -84,7 +84,7 @@ process DIANN { if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { error "DIANN module does not support Conda. Please use Docker / Singularity / Podman instead." } - def prefix = task.ext.prefix ?: "${meta.id}" ?: "diann" + prefix = task.ext.prefix ?: "${meta.id}" ?: "diann" """ # Library outputs diff --git a/modules/nf-core/eklipse/main.nf b/modules/nf-core/eklipse/main.nf index 98c5778953d7..07f73ca4d5d4 100644 --- a/modules/nf-core/eklipse/main.nf +++ b/modules/nf-core/eklipse/main.nf @@ -25,14 +25,14 @@ process EKLIPSE { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def ref_gb = ref_gb ? "$ref_gb" : "/usr/local/bin/data/NC_012920.1.gb" + def ref_gb_path = ref_gb ? "$ref_gb" : "/usr/local/bin/data/NC_012920.1.gb" def VERSION = "1.8" // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. """ echo "$bam\t${prefix}" > infile.txt eKLIPse.py \\ -in infile.txt \\ $args \\ - -ref $ref_gb + -ref $ref_gb_path mv eKLIPse_*/eKLIPse_deletions.csv eKLIPse_${prefix}_deletions.csv mv eKLIPse_*/eKLIPse_genes.csv eKLIPse_${prefix}_genes.csv mv eKLIPse_*/eKLIPse_${prefix}.png eKLIPse_${prefix}.png diff --git a/modules/nf-core/flash/main.nf b/modules/nf-core/flash/main.nf index ca67151a3e87..7d31185f3f8b 100644 --- a/modules/nf-core/flash/main.nf +++ b/modules/nf-core/flash/main.nf @@ -42,7 +42,7 @@ process FLASH { stub: - def prefix = task.ext.prefix ?: "${meta.id}" + prefix = task.ext.prefix ?: "${meta.id}" """ echo "" | gzip > ${prefix}.fastq.gz diff --git a/modules/nf-core/gmmdemux/main.nf b/modules/nf-core/gmmdemux/main.nf index 6da98713cf40..f2b9186a7cb3 100644 --- a/modules/nf-core/gmmdemux/main.nf +++ b/modules/nf-core/gmmdemux/main.nf @@ -30,10 +30,10 @@ process GMMDEMUX { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def skip = skip ? "--skip $skip" : "" + def skip_opt = skip ? "--skip $skip" : "" def examine_cells = examine ? "--examine $examine" : "" def VERSION = '0.2.2.3' // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. - def type_report = type_report ? "-f ." : "-s ." + def type_report_opt = type_report ? "-f ." : "-s ." def summary_rep = summary_report ? "-r ${prefix}_summary_report.txt" : "" """ if [[ ${summary_report} == true ]]; then @@ -41,9 +41,9 @@ process GMMDEMUX { fi GMM-demux $args \\ - $type_report \\ + $type_report_opt \\ $summary_rep \\ - $skip \\ + $skip_opt \\ $examine_cells \\ $hto_matrix \\ $hto_names \\ diff --git a/modules/nf-core/happy/sompy/main.nf b/modules/nf-core/happy/sompy/main.nf index ba23fd16765d..f5b522cec521 100644 --- a/modules/nf-core/happy/sompy/main.nf +++ b/modules/nf-core/happy/sompy/main.nf @@ -32,7 +32,7 @@ process HAPPY_SOMPY { def targets = targets_bed ? "-T ${targets_bed}" : "" def false_positives = false_positives_bed ? "--false-positives ${false_positives_bed}" : "" def ambiguous = ambiguous_beds ? "--ambiguous ${ambiguous_beds}" : "" - def bams = bams ? "--bam ${bams}" : "" + def bams_opt = bams ? "--bam ${bams}" : "" def VERSION = '0.3.14' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. """ som.py \\ @@ -44,7 +44,7 @@ process HAPPY_SOMPY { ${targets} \\ ${false_positives} \\ ${ambiguous} \\ - ${bams} \\ + ${bams_opt} \\ -o ${prefix} cat <<-END_VERSIONS > versions.yml diff --git a/modules/nf-core/hmmer/hmmfetch/main.nf b/modules/nf-core/hmmer/hmmfetch/main.nf index d35638b7d6d8..6648b3d7c313 100644 --- a/modules/nf-core/hmmer/hmmfetch/main.nf +++ b/modules/nf-core/hmmer/hmmfetch/main.nf @@ -29,13 +29,13 @@ process HMMER_HMMFETCH { def prefix = task.ext.prefix ?: "${meta.id}" def keyarg = key ?: '' def kfopt = keyfile ? '-f' : '' - def index = ! key && ! keyfile ? '--index' : '' + def index_opt = ! key && ! keyfile ? '--index' : '' def outfile = ! key && ! keyfile ? '' : "> ${prefix}.hmm" """ hmmfetch \\ $kfopt \\ - $index \\ + $index_opt \\ $args \\ $hmm \\ $keyarg \\ diff --git a/modules/nf-core/hmmer/hmmfetch/tests/main.nf.test b/modules/nf-core/hmmer/hmmfetch/tests/main.nf.test index 46c7b58fcc21..8f18266ee810 100644 --- a/modules/nf-core/hmmer/hmmfetch/tests/main.nf.test +++ b/modules/nf-core/hmmer/hmmfetch/tests/main.nf.test @@ -17,7 +17,7 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:false ], - file('https://raw.githubusercontent.com/tseemann/barrnap/master/db/arc.hmm') + file('https://raw.githubusercontent.com/tseemann/barrnap/0.9/db/arc.hmm', checkIfExists: true) ] input[1] = '16S_rRNA' input[2] = [] @@ -44,7 +44,7 @@ nextflow_process { input[0] = [ [ id:'test', single_end:false ], - file('https://raw.githubusercontent.com/tseemann/barrnap/master/db/arc.hmm') + file('https://raw.githubusercontent.com/tseemann/barrnap/0.9/db/arc.hmm', checkIfExists: true) ] input[1] = [] input[2] = keyfile @@ -69,7 +69,7 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:false ], - file('https://raw.githubusercontent.com/tseemann/barrnap/master/db/arc.hmm') + file('https://raw.githubusercontent.com/tseemann/barrnap/0.9/db/arc.hmm', checkIfExists: true) ] input[1] = [] input[2] = [] @@ -94,7 +94,7 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:false ], - file('https://raw.githubusercontent.com/tseemann/barrnap/master/db/arc.hmm') + file('https://raw.githubusercontent.com/tseemann/barrnap/0.9/db/arc.hmm', checkIfExists: true) ] input[1] = [] input[2] = [] diff --git a/modules/nf-core/hmmer/hmmrank/tests/main.nf.test b/modules/nf-core/hmmer/hmmrank/tests/main.nf.test index eb1b04895170..b44225d7d691 100644 --- a/modules/nf-core/hmmer/hmmrank/tests/main.nf.test +++ b/modules/nf-core/hmmer/hmmrank/tests/main.nf.test @@ -20,8 +20,8 @@ nextflow_process { process { """ input[0] = Channel.fromList([ - tuple([ id: 'arc16s' ], file("https://raw.githubusercontent.com/tseemann/barrnap/master/db/arc.hmm")), - tuple([ id: 'bac16s' ], file("https://raw.githubusercontent.com/tseemann/barrnap/master/db/bac.hmm")) + tuple([ id: 'arc16s' ], file("https://raw.githubusercontent.com/tseemann/barrnap/0.9/db/arc.hmm", checkIfExists: true)), + tuple([ id: 'bac16s' ], file("https://raw.githubusercontent.com/tseemann/barrnap/0.9/db/bac.hmm", checkIfExists: true)) ]) input[1] = Channel.of('16S_rRNA').first() input[2] = [] diff --git a/modules/nf-core/hmmer/hmmrank/tests/main.nf.test.snap b/modules/nf-core/hmmer/hmmrank/tests/main.nf.test.snap index faaa61a4c1e1..23ea5c261014 100644 --- a/modules/nf-core/hmmer/hmmrank/tests/main.nf.test.snap +++ b/modules/nf-core/hmmer/hmmrank/tests/main.nf.test.snap @@ -19,7 +19,7 @@ { "id": "16S-test" }, - "16S-test.hmmrank.tsv.gz:md5,b4f48685b5b0127114c68dda279c0cbd" + "16S-test.hmmrank.tsv.gz:md5,ee4e777c815c37727358ab4ebda276b3" ] ], "1": [ @@ -30,7 +30,7 @@ { "id": "16S-test" }, - "16S-test.hmmrank.tsv.gz:md5,b4f48685b5b0127114c68dda279c0cbd" + "16S-test.hmmrank.tsv.gz:md5,ee4e777c815c37727358ab4ebda276b3" ] ], "versions": [ @@ -51,7 +51,7 @@ { "id": "16S-test" }, - "16S-test.hmmrank.tsv.gz:md5,b4f48685b5b0127114c68dda279c0cbd" + "16S-test.hmmrank.tsv.gz:md5,ee4e777c815c37727358ab4ebda276b3" ] ] ], diff --git a/modules/nf-core/ichorcna/createpon/main.nf b/modules/nf-core/ichorcna/createpon/main.nf index 3be817e0c2cd..a8b4673ec311 100644 --- a/modules/nf-core/ichorcna/createpon/main.nf +++ b/modules/nf-core/ichorcna/createpon/main.nf @@ -28,7 +28,7 @@ process ICHORCNA_CREATEPON { def map = map_wig ? "mapWig='${map_wig}'," : 'mapWig=NULL,' def centro = centromere ? "centromere='${centromere}'," : '' def rep = rep_time_wig ? "repTimeWig='${rep_time_wig}'," : 'repTimeWig=NULL,' - def exons = exons ? "exons.bed='${exons}'," : '' + def exons_opt = exons ? "exons.bed='${exons}'," : '' """ #!/usr/bin/env Rscript @@ -43,7 +43,7 @@ process ICHORCNA_CREATEPON { ${rep} filelist = "filelist.txt", outfile = "${prefix}", - ${exons} + ${exons_opt} ${centro} $args ) diff --git a/modules/nf-core/igvreports/main.nf b/modules/nf-core/igvreports/main.nf index b47846e444bb..1a2ce7fb681c 100644 --- a/modules/nf-core/igvreports/main.nf +++ b/modules/nf-core/igvreports/main.nf @@ -21,7 +21,7 @@ process IGVREPORTS { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def fasta = fasta ? "--fasta ${fasta}" : "" + def fasta_opt = fasta ? "--fasta ${fasta}" : "" // If tracks is not null, create a string of the track paths def track_arg = tracks ? "--tracks "+ tracks.collect { it.toString() }.join(' ') : "" // if "--tracks" is in the args, then add track_string immediately after it in @@ -34,7 +34,7 @@ process IGVREPORTS { """ create_report $sites \ $args \ - $fasta \ + $fasta_opt \ $track_arg \ --output ${prefix}_report.html diff --git a/modules/nf-core/jvarkit/sam2tsv/main.nf b/modules/nf-core/jvarkit/sam2tsv/main.nf index fdc49cbd8bad..d9d9d261b325 100644 --- a/modules/nf-core/jvarkit/sam2tsv/main.nf +++ b/modules/nf-core/jvarkit/sam2tsv/main.nf @@ -21,7 +21,7 @@ process JVARKIT_SAM2TSV { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def regions_file = regions_file ? " --regions" + " '${regions_file}' " : "" + def regions_opt = regions_file ? " --regions" + " '${regions_file}' " : "" """ mkdir -p TMP @@ -30,7 +30,7 @@ process JVARKIT_SAM2TSV { --reference "${fasta}" \\ --output "${prefix}.tsv" \\ ${args} \\ - ${regions_file} \\ + ${regions_opt} \\ "${bam}" rm -rf TMP diff --git a/modules/nf-core/jvarkit/vcf2table/main.nf b/modules/nf-core/jvarkit/vcf2table/main.nf index f701a6b487ef..5179979843a3 100644 --- a/modules/nf-core/jvarkit/vcf2table/main.nf +++ b/modules/nf-core/jvarkit/vcf2table/main.nf @@ -22,14 +22,14 @@ process JVARKIT_VCF2TABLE { def args2 = task.ext.args2 ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def ped = pedigree?"--pedigree \"${pedigree}\"":"" - def regions_file = regions_file? (tbi ? " --regions-file" : " --targets-file")+" \"${regions_file}\" ":"" + def regions_opt = regions_file? (tbi ? " --regions-file" : " --targets-file")+" \"${regions_file}\" ":"" extension = getFileExtension(args2); /* custom function, see below */ if ("$vcf" == "${prefix}.${extension}") error "Input and output names are the same, set prefix in module configuration to disambiguate!" """ mkdir -p TMP - bcftools view ${regions_file} -O v ${args1} "${vcf}" |\\ + bcftools view ${regions_opt} -O v ${args1} "${vcf}" |\\ jvarkit -Xmx${task.memory.giga}g -XX:-UsePerfData -Djava.io.tmpdir=TMP vcf2table ${ped} ${args2} > "${prefix}.${extension}" rm -rf TMP diff --git a/modules/nf-core/krakentools/extractkrakenreads/main.nf b/modules/nf-core/krakentools/extractkrakenreads/main.nf index 7c048c062788..9fa8a9c0c779 100644 --- a/modules/nf-core/krakentools/extractkrakenreads/main.nf +++ b/modules/nf-core/krakentools/extractkrakenreads/main.nf @@ -11,8 +11,8 @@ process KRAKENTOOLS_EXTRACTKRAKENREADS { input: val taxid // Separated by spaces tuple val(meta), path(classified_reads_assignment) - tuple val(meta), path(classified_reads_fastq) - tuple val(meta), path(report) + tuple val(meta2), path(classified_reads_fastq) + tuple val(meta3), path(report) output: tuple val(meta), path("*.{fastq.gz,fasta.gz}"), emit: extracted_kraken2_reads diff --git a/modules/nf-core/krakentools/extractkrakenreads/meta.yml b/modules/nf-core/krakentools/extractkrakenreads/meta.yml index 720868b2552b..b29d14038c19 100644 --- a/modules/nf-core/krakentools/extractkrakenreads/meta.yml +++ b/modules/nf-core/krakentools/extractkrakenreads/meta.yml @@ -29,7 +29,7 @@ input: description: A file contains the taxonomic classification of each input read. pattern: "*.{classifiedreads.txt}" ontologies: [] - - - meta: + - - meta2: type: map description: | Groovy Map containing sample information @@ -40,7 +40,7 @@ input: database. pattern: "*.{fastq.gz}" ontologies: [] - - - meta: + - - meta3: type: map description: | Groovy Map containing sample information diff --git a/modules/nf-core/mafft/align/main.nf b/modules/nf-core/mafft/align/main.nf index de939039ac44..e21a30254304 100644 --- a/modules/nf-core/mafft/align/main.nf +++ b/modules/nf-core/mafft/align/main.nf @@ -25,24 +25,24 @@ process MAFFT_ALIGN { task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - add = add ? "--add <(unpigz -cdf ${add})" : '' - addfragments = addfragments ? "--addfragments <(unpigz -cdf ${addfragments})" : '' - addfull = addfull ? "--addfull <(unpigz -cdf ${addfull})" : '' - addprofile = addprofile ? "--addprofile <(unpigz -cdf ${addprofile})" : '' - addlong = addlong ? "--addlong <(unpigz -cdf ${addlong})" : '' - write_output = compress ? " | pigz -cp ${task.cpus} > ${prefix}.fas.gz" : "> ${prefix}.fas" + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def add_opt = add ? "--add <(unpigz -cdf ${add})" : '' + def addfragments_opt = addfragments ? "--addfragments <(unpigz -cdf ${addfragments})" : '' + def addfull_opt = addfull ? "--addfull <(unpigz -cdf ${addfull})" : '' + def addprofile_opt = addprofile ? "--addprofile <(unpigz -cdf ${addprofile})" : '' + def addlong_opt = addlong ? "--addlong <(unpigz -cdf ${addlong})" : '' + def write_output = compress ? " | pigz -cp ${task.cpus} > ${prefix}.fas.gz" : "> ${prefix}.fas" // this will not preserve MAFFTs return value, but mafft crashes when it receives a process substitution if ("$fasta" == "${prefix}.fas" ) error "Input and output names are the same, set prefix in module configuration to disambiguate!" """ mafft \\ --thread ${task.cpus} \\ - ${add} \\ - ${addfragments} \\ - ${addfull} \\ - ${addprofile} \\ - ${addlong} \\ + ${add_opt} \\ + ${addfragments_opt} \\ + ${addfull_opt} \\ + ${addprofile_opt} \\ + ${addlong_opt} \\ ${args} \\ ${fasta} \\ ${write_output} diff --git a/modules/nf-core/peka/environment.yml b/modules/nf-core/peka/environment.yml index 28c52d4b706e..b38d3fc17cd9 100644 --- a/modules/nf-core/peka/environment.yml +++ b/modules/nf-core/peka/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::peka=1.0.0 + - bioconda::peka=1.0.2 diff --git a/modules/nf-core/peka/main.nf b/modules/nf-core/peka/main.nf index f1e0c80eed3a..8e7bb45dea38 100644 --- a/modules/nf-core/peka/main.nf +++ b/modules/nf-core/peka/main.nf @@ -4,12 +4,12 @@ process PEKA { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/peka:1.0.0--pyhdfd78af_0': - 'biocontainers/peka:1.0.0--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/peka:1.0.2--pyhdfd78af_0': + 'biocontainers/peka:1.0.2--pyhdfd78af_0' }" input: tuple val(meta), path(peaks) - tuple val(meta), path(crosslinks) + tuple val(meta2), path(crosslinks) path fasta path fai path gtf @@ -29,7 +29,7 @@ process PEKA { script: def args = task.ext.args ?: '' - def VERSION = '1.0.0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. + def VERSION = '1.0.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. """ # If the modification date and time of the fai is before the fasta then # there will be an error. Touching the file first avoids that. @@ -51,7 +51,7 @@ process PEKA { stub: def prefix = task.ext.prefix ?: "${meta.id}" - def VERSION = '1.0.0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. + def VERSION = '1.0.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. """ touch ${prefix}_4mer_cluster_distribution_genome.tsv touch ${prefix}_4mer_distribution_genome.tsv diff --git a/modules/nf-core/peka/meta.yml b/modules/nf-core/peka/meta.yml index 7a36a252d1be..4cf52984703d 100644 --- a/modules/nf-core/peka/meta.yml +++ b/modules/nf-core/peka/meta.yml @@ -27,7 +27,7 @@ input: description: BED file of peak regions pattern: "*.{bed,bed.gz}" ontologies: [] - - - meta: + - - meta2: type: map description: | Groovy Map containing sample information diff --git a/modules/nf-core/peka/tests/main.nf.test.snap b/modules/nf-core/peka/tests/main.nf.test.snap index 4fc45ddd778c..1bb2fbbaae83 100644 --- a/modules/nf-core/peka/tests/main.nf.test.snap +++ b/modules/nf-core/peka/tests/main.nf.test.snap @@ -5,7 +5,7 @@ "chr21_HepG2-PCBP1-merged_4mer_distribution_genome.tsv", "chr21_HepG2-PCBP1-merged_4mer_genome.pdf", [ - "versions.yml:md5,2640fd0e434e4446101fd4dc617af54b" + "versions.yml:md5,06fe7ab1f3425110fff0e21871b484fa" ] ], "meta": { @@ -54,7 +54,7 @@ ], "7": [ - "versions.yml:md5,2640fd0e434e4446101fd4dc617af54b" + "versions.yml:md5,06fe7ab1f3425110fff0e21871b484fa" ], "clust": [ @@ -93,7 +93,7 @@ ], "versions": [ - "versions.yml:md5,2640fd0e434e4446101fd4dc617af54b" + "versions.yml:md5,06fe7ab1f3425110fff0e21871b484fa" ] } ], diff --git a/modules/nf-core/pureclip/main.nf b/modules/nf-core/pureclip/main.nf index 71acb9a6669f..3e5e9c9739fe 100644 --- a/modules/nf-core/pureclip/main.nf +++ b/modules/nf-core/pureclip/main.nf @@ -9,8 +9,8 @@ process PURECLIP { input: tuple val(meta), path(ipbam), path(controlbam) - tuple val(meta), path(ipbai), path(controlbai) - tuple val(meta2), path(genome_fasta) + tuple val(meta2), path(ipbai), path(controlbai) + tuple val(meta3), path(genome_fasta) val input_control output: diff --git a/modules/nf-core/pureclip/meta.yml b/modules/nf-core/pureclip/meta.yml index e6548ba7f36b..8c2c88c580cb 100644 --- a/modules/nf-core/pureclip/meta.yml +++ b/modules/nf-core/pureclip/meta.yml @@ -31,7 +31,7 @@ input: description: Sorted BAM/CRAM/SAM file pattern: "*.{bam,cram,sam}" ontologies: [] - - - meta: + - - meta2: type: map description: | Groovy Map containing sample information @@ -46,7 +46,7 @@ input: description: BAM index pattern: "*.{bai}" ontologies: [] - - - meta2: + - - meta3: type: map description: | Groovy Map containing reference information. diff --git a/modules/nf-core/salsa2/main.nf b/modules/nf-core/salsa2/main.nf index 876aaad5c5cc..7f8f02683ba9 100644 --- a/modules/nf-core/salsa2/main.nf +++ b/modules/nf-core/salsa2/main.nf @@ -27,8 +27,8 @@ process SALSA2 { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def gfa = gfa ? "--gfa $gfa" : "" - def dup = dup ? "--dup $dup" : "" + def gfa_opt = gfa ? "--gfa $gfa" : "" + def dup_opt = dup ? "--dup $dup" : "" def filter = filter_bed ? "--filter $filter_bed" : "" def VERSION = '2.3' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. """ @@ -37,8 +37,8 @@ process SALSA2 { --assembly $fasta \\ --bed $bed \\ --length $index \\ - $gfa \\ - $dup \\ + $gfa_opt \\ + $dup_opt \\ $filter mv */scaffolds_FINAL.fasta ${prefix}_scaffolds_FINAL.fasta diff --git a/modules/nf-core/sam2lca/analyze/main.nf b/modules/nf-core/sam2lca/analyze/main.nf index aabeee9e704d..9ada571b08a6 100644 --- a/modules/nf-core/sam2lca/analyze/main.nf +++ b/modules/nf-core/sam2lca/analyze/main.nf @@ -25,11 +25,11 @@ process SAM2LCA_ANALYZE { def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def make_db = database ? "" : "mkdir sam2lca_db" - def database = database ? "${database}" : "sam2lca_db" + def database_path = database ? "${database}" : "sam2lca_db" """ $make_db sam2lca \\ - -d $database \\ + -d $database_path \\ analyze \\ $args \\ -o ${prefix} \\ diff --git a/modules/nf-core/scds/main.nf b/modules/nf-core/scds/main.nf index a9be3157eae6..ceea7023a395 100644 --- a/modules/nf-core/scds/main.nf +++ b/modules/nf-core/scds/main.nf @@ -24,7 +24,7 @@ process SCDS { template 'scds.R' stub: - def prefix = task.ext.prefix ?: "${meta.id}" + prefix = task.ext.prefix ?: "${meta.id}" if ("${rds}" == "${prefix}.rds") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" """ touch ${prefix}.rds diff --git a/modules/nf-core/scds/tests/main.nf.test b/modules/nf-core/scds/tests/main.nf.test index 6fce391f6e3c..97fd74adc450 100644 --- a/modules/nf-core/scds/tests/main.nf.test +++ b/modules/nf-core/scds/tests/main.nf.test @@ -13,7 +13,7 @@ nextflow_process { """ input[0] = [ [ id:'test' ], // meta map - file("https://raw.githubusercontent.com/nf-core/test-datasets/scdownstream/samples/SAMN14430801_custom_emptydrops_filter_matrix_sce.rds", checkIfExists: true) + file("https://github.com/nf-core/test-datasets/raw/e92fd1399f7ef839e075c09762f55cace91b8485/samples/SAMN14430801_custom_emptydrops_filter_matrix_sce.rds", checkIfExists: true) ] """ } @@ -34,7 +34,7 @@ nextflow_process { """ input[0] = [ [ id:'test' ], // meta map - file("https://raw.githubusercontent.com/nf-core/test-datasets/scdownstream/samples/SAMN14430801_custom_emptydrops_filter_matrix_sce.rds", checkIfExists: true) + file("https://github.com/nf-core/test-datasets/raw/e92fd1399f7ef839e075c09762f55cace91b8485/samples/SAMN14430801_custom_emptydrops_filter_matrix_sce.rds", checkIfExists: true) ] """ } diff --git a/modules/nf-core/segemehl/align/main.nf b/modules/nf-core/segemehl/align/main.nf index fa829a73a160..b486d3f535d5 100644 --- a/modules/nf-core/segemehl/align/main.nf +++ b/modules/nf-core/segemehl/align/main.nf @@ -25,7 +25,7 @@ process SEGEMEHL_ALIGN { script: def args = task.ext.args ?: '' prefix = task.ext.prefix ?: "${meta.id}" - def reads = meta.single_end ? "-q ${reads}" : "-q ${reads[0]} -p ${reads[1]}" + def reads_opt = meta.single_end ? "-q ${reads}" : "-q ${reads[0]} -p ${reads[1]}" suffix = ( args.contains("-b") || args.contains("--bamabafixoida") ) ? "bam" : "sam" """ mkdir -p $prefix @@ -34,7 +34,7 @@ process SEGEMEHL_ALIGN { -t $task.cpus \\ -d $fasta \\ -i $index \\ - $reads \\ + $reads_opt \\ $args \\ -o ${prefix}/${prefix}.${suffix} diff --git a/modules/nf-core/spaceranger/count/main.nf b/modules/nf-core/spaceranger/count/main.nf index 246f3364e43d..ae26942e1d7f 100644 --- a/modules/nf-core/spaceranger/count/main.nf +++ b/modules/nf-core/spaceranger/count/main.nf @@ -24,14 +24,14 @@ process SPACERANGER_COUNT { def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" // Add flags for optional inputs on demand. - def probeset = probeset ? "--probe-set=\"${probeset}\"" : "" - def alignment = alignment ? "--loupe-alignment=\"${alignment}\"" : "" - def slidefile = slidefile ? "--slidefile=\"${slidefile}\"" : "" - def image = image ? "--image=\"${image}\"" : "" - def cytaimage = cytaimage ? "--cytaimage=\"${cytaimage}\"" : "" - def darkimage = darkimage ? "--darkimage=\"${darkimage}\"" : "" - def colorizedimage = colorizedimage ? "--colorizedimage=\"${colorizedimage}\"" : "" - if (slide.matches("visium-(.*)") && area == "" && slidefile == "") { + def probeset_opt = probeset ? "--probe-set=\"${probeset}\"" : "" + def alignment_opt = alignment ? "--loupe-alignment=\"${alignment}\"" : "" + def slidefile_opt = slidefile ? "--slidefile=\"${slidefile}\"" : "" + def image_opt = image ? "--image=\"${image}\"" : "" + def cytaimage_opt = cytaimage ? "--cytaimage=\"${cytaimage}\"" : "" + def darkimage_opt = darkimage ? "--darkimage=\"${darkimage}\"" : "" + def colorizedimage_opt = colorizedimage ? "--colorizedimage=\"${colorizedimage}\"" : "" + if (slide.matches("visium-(.*)") && area == "" && slidefile_opt == "") { slide_and_area = "--unknown-slide=\"${slide}\"" } else { slide_and_area = "--slide=\"${slide}\" --area=\"${area}\"" @@ -44,11 +44,14 @@ process SPACERANGER_COUNT { --transcriptome="${reference}" \\ --localcores=${task.cpus} \\ --localmem=${task.memory.toGiga()} \\ - $image $cytaimage $darkimage $colorizedimage \\ + $image_opt \\ + $cytaimage_opt \\ + $darkimage_opt \\ + $colorizedimage_opt \\ $slide_and_area \\ - $probeset \\ - $alignment \\ - $slidefile \\ + $probeset_opt \\ + $alignment_opt \\ + $slidefile_opt \\ $args mv ${prefix}/outs outs diff --git a/modules/nf-core/svanalyzer/svbenchmark/main.nf b/modules/nf-core/svanalyzer/svbenchmark/main.nf index b9cb25ff1022..c5de76296223 100644 --- a/modules/nf-core/svanalyzer/svbenchmark/main.nf +++ b/modules/nf-core/svanalyzer/svbenchmark/main.nf @@ -33,7 +33,7 @@ process SVANALYZER_SVBENCHMARK { def args = task.ext.args ?: '' def args2 = task.ext.args2 ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def bed = bed ? "-includebed $bed" : "" + def bed_opt = bed ? "-includebed $bed" : "" def VERSION = '0.36' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. """ @@ -44,7 +44,7 @@ process SVANALYZER_SVBENCHMARK { --test $test \\ --truth $truth \\ --prefix $prefix \\ - $bed + $bed_opt bgzip ${args2} --threads ${task.cpus} -c ${prefix}.falsenegatives.vcf > ${prefix}.falsenegatives.vcf.gz bgzip ${args2} --threads ${task.cpus} -c ${prefix}.falsepositives.vcf > ${prefix}.falsepositives.vcf.gz diff --git a/modules/nf-core/svtyper/svtyper/main.nf b/modules/nf-core/svtyper/svtyper/main.nf index ffc2c9cf395d..2b9fe2965c89 100644 --- a/modules/nf-core/svtyper/svtyper/main.nf +++ b/modules/nf-core/svtyper/svtyper/main.nf @@ -10,7 +10,7 @@ process SVTYPER_SVTYPER { input: tuple val(meta), path(bam), path(bam_index), path(vcf) tuple val(meta2), path(fasta) - tuple val(meta2), path(fai) + tuple val(meta3), path(fai) output: tuple val(meta), path("*.json"), emit: json @@ -24,13 +24,13 @@ process SVTYPER_SVTYPER { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def vcf = vcf ? "--input_vcf ${vcf}" : "" + def vcf_opt = vcf ? "--input_vcf ${vcf}" : "" if ("$vcf" == "${prefix}.vcf") error "Input and output names are the same, set prefix in module configuration to disambiguate!" if ("$bam" == "${prefix}.bam") error "Input and output names are the same, set prefix in module configuration to disambiguate!" """ svtyper \\ - $vcf \\ + $vcf_opt \\ --bam $bam \\ --lib_info ${prefix}.json \\ --output_vcf ${prefix}.vcf \\ diff --git a/modules/nf-core/svtyper/svtyper/meta.yml b/modules/nf-core/svtyper/svtyper/meta.yml index bad90d436d32..cd9b215bb48d 100644 --- a/modules/nf-core/svtyper/svtyper/meta.yml +++ b/modules/nf-core/svtyper/svtyper/meta.yml @@ -45,7 +45,7 @@ input: description: FASTA file used to generate alignments pattern: "*.{fa,fasta}" ontologies: [] - - - meta2: + - - meta3: type: map description: | Groovy Map containing sample information for FASTA file diff --git a/modules/nf-core/svtyper/svtypersso/main.nf b/modules/nf-core/svtyper/svtypersso/main.nf index 123a12495b9f..60d662f468b2 100644 --- a/modules/nf-core/svtyper/svtypersso/main.nf +++ b/modules/nf-core/svtyper/svtypersso/main.nf @@ -22,15 +22,15 @@ process SVTYPER_SVTYPERSSO { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def vcf = vcf ? "--input_vcf ${vcf}" : "" - def fasta = fasta ? "--ref_fasta ${fasta}" : "" + def vcf_opt = vcf ? "--input_vcf ${vcf}" : "" + def fasta_opt = fasta ? "--ref_fasta ${fasta}" : "" if ("$vcf" == "${prefix}.vcf") error "Input and output names are the same, set prefix in module configuration to disambiguate!" if ("$bam" == "${prefix}.bam") error "Input and output names are the same, set prefix in module configuration to disambiguate!" """ svtyper-sso \\ --bam $bam \\ - $vcf \\ - $fasta \\ + $vcf_opt \\ + $fasta_opt \\ --output_vcf ${prefix}.vcf \\ --lib_info ${prefix}.json \\ --cores $task.cpus \\ diff --git a/modules/nf-core/svtyper/svtypersso/tests/main.nf.test.snap b/modules/nf-core/svtyper/svtypersso/tests/main.nf.test.snap index e83a9345e89f..5bed7fda1cfd 100644 --- a/modules/nf-core/svtyper/svtypersso/tests/main.nf.test.snap +++ b/modules/nf-core/svtyper/svtypersso/tests/main.nf.test.snap @@ -55,7 +55,7 @@ { "id": "test" }, - "test.vcf:md5,aee556ba714a2a3d64fb4fc9f2753cea" + "test.vcf:md5,2a50aac58a80c25a05a13f676afbc875" ] ], [ @@ -75,7 +75,7 @@ { "id": "test" }, - "test.vcf:md5,b4a4e316e8524535ca1d3f26ad39ac78" + "test.vcf:md5,73a3555ad43a26f252137bfbd9f07a93" ] ], [