Fix variable redeclarations for strict syntax compliance (from branch)

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
 

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

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 == "[]" ):
 

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

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}":

modules/nf-core/crumble/main.nf

@@ -30,15 +30,15 @@ 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.
     """
     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}":

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

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",
             [

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

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

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

modules/nf-core/gmmdemux/main.nf

@@ -30,20 +30,20 @@ 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
         cat /dev/null > ${prefix}_summary_report.txt
     fi
 
     GMM-demux $args \\
-        $type_report \\
+        $type_report_opt \\
         $summary_rep \\
-        $skip \\
+        $skip_opt \\
         $examine_cells \\
         $hto_matrix \\
         $hto_names \\

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

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 \\

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] = []

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] = []

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"
                 ]
             ]
         ],

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
     )

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
 

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