Update for v25.11.0-edge

CHANGELOG.md

@@ -9,7 +9,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - Addition of `params.multi_mapping` to change the level of multi-mapping filtering performed by PretextMap.
   - This corresponds to the mapq (mapping quality) value.
-- Updated `trace` scope to start collecting SummaryStat data again.
+- Updated `t
+- production { includeConfig 'conf/production.config' }race` scope to start collecting SummaryStat data again.
 
 ### Paramters
 

modules/local/cram/filter_align_bwamem2_fixmate_sort/main.nf

@@ -18,9 +18,9 @@ process CRAM_FILTER_ALIGN_BWAMEM2_FIXMATE_SORT {
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
+    def _args = task.ext.args ?: ''
     def args1 = task.ext.args1 ?: ''
-    def args2 = task.ext.args2 ?: ''
+    def _args2 = task.ext.args2 ?: ''
     def args3 = task.ext.args3 ?: ''
     def args4 = task.ext.args4 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
@@ -43,8 +43,6 @@ process CRAM_FILTER_ALIGN_BWAMEM2_FIXMATE_SORT {
 
     stub:
     def prefix  = task.ext.prefix ?: "${meta.id}"
-    def base    = "45022_3#2"
-    def chunkid = "1"
     """
     touch ${prefix}_${base}_${chunkid}_mem.bam
 

modules/local/cram/filter_minimap2_filter5end_fixmate_sort/main.nf

@@ -18,7 +18,7 @@ process CRAM_FILTER_MINIMAP2_FILTER5END_FIXMATE_SORT {
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
+    def _args = task.ext.args ?: ''
     def args1 = task.ext.args1 ?: ''
     def args2 = task.ext.args2 ?: ''
     def args3 = task.ext.args3 ?: ''
@@ -44,8 +44,6 @@ process CRAM_FILTER_MINIMAP2_FILTER5END_FIXMATE_SORT {
 
     stub:
     def prefix  = task.ext.prefix ?: "${meta.id}"
-    def base    = "45022_3#2"
-    def chunkid = "1"
     """
     touch ${prefix}_${base}_${chunkid}_mm.bam
 

modules/local/find/telomere_windows/main.nf

@@ -22,7 +22,7 @@ process FIND_TELOMERE_WINDOWS {
     def VERSION = "1.0" // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     def telomere_jar = task.ext.telomere_jar ?: ''
     def telomere_jvm_params = task.ext.telomere_jvm_params ?: ''
-    def telomere_window_cut = task.ext.telomere_window_cut ?: 99.9
+    def telomere_window_cut = task.ext.telomere_window_cut ?: "99.9"
     """
     java ${telomere_jvm_params} -cp ${projectDir}/bin/${telomere_jar} FindTelomereWindows $file $telomere_window_cut > ${prefix}.windows
 
@@ -35,7 +35,6 @@ process FIND_TELOMERE_WINDOWS {
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     def VERSION = "1.0" // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
-    def telomere = task.ext.telomere ?: ''
     """
     touch ${prefix}.windows
 

modules/local/gawk_split_directions/main.nf

@@ -23,12 +23,12 @@ process GAWK_SPLIT_DIRECTIONS {
     def args  = task.ext.args  ?: '' // args is used for the main arguments of the tool
     def args2 = task.ext.args2 ?: '' // args2 is used to specify a program when no program file has been given
     prefix    = task.ext.prefix ?: "${meta.id}"
-    suffix    = task.ext.suffix ?: "${input.collect{ it.getExtension()}.get(0)}" // use the first extension of the input files
+    suffix    = task.ext.suffix ?: "${input.collect{ file -> file.getExtension()}.get(0)}" // use the first extension of the input files
 
     program    = program_file ? "-f ${program_file}" : "${args2}"
 
-    input.collect{
-        assert it.name != "${prefix}.${suffix}" : "Input and output names are the same, set prefix in module configuration to disambiguate!"
+    input.collect{ file ->
+        assert file.name != "${prefix}.${suffix}" : "Input and output names are the same, set prefix in module configuration to disambiguate!"
     }
 
     """

nextflow.config

@@ -34,9 +34,9 @@ params {
     plaintext_email            = false
     monochrome_logs            = false
     hook_url                   = null
-    help                         = false
-    help_full                    = false
-    show_hidden                  = false
+    help                       = false
+    help_full                  = false
+    show_hidden                = false
     version                    = false
     validate_params            = true
 
@@ -217,7 +217,7 @@ process.shell = [
 // Disable process selector warnings by default. Use debug profile to enable warnings.
 nextflow.enable.configProcessNamesValidation = false
 
-def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss' )
+//def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss' )
 timeline {
     enabled = true
     file    = "${params.outdir}/pipeline_info/execution_timeline_${params.trace_report_suffix}.html"
@@ -293,31 +293,31 @@ validation {
         command = "nextflow run sanger-tol/curationpretext -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
         fullParameter = "help_full"
         showHiddenParameter = "show_hidden"
-        beforeText = """
--\033[2m----------------------------------------------------\033[0m-
-\033[0;34m   _____                               \033[0;32m _______   \033[0;31m _\033[0m
-\033[0;34m  / ____|                              \033[0;32m|__   __|  \033[0;31m| |\033[0m
-\033[0;34m | (___   __ _ _ __   __ _  ___ _ __ \033[0m ___ \033[0;32m| |\033[0;33m ___ \033[0;31m| |\033[0m
-\033[0;34m  \\___ \\ / _` | '_ \\ / _` |/ _ \\ '__|\033[0m|___|\033[0;32m| |\033[0;33m/ _ \\\033[0;31m| |\033[0m
-\033[0;34m  ____) | (_| | | | | (_| |  __/ |        \033[0;32m| |\033[0;33m (_) \033[0;31m| |____\033[0m
-\033[0;34m |_____/ \\__,_|_| |_|\\__, |\\___|_|        \033[0;32m|_|\033[0;33m\\___/\033[0;31m|______|\033[0m
-\033[0;34m                      __/ |\033[0m
-\033[0;34m                     |___/\033[0m
-\033[0;35m  ${manifest.name} ${manifest.version}\033[0m
--\033[2m----------------------------------------------------\033[0m-
-"""
-    afterText = """${manifest.doi ? "\n* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "    https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
-* The nf-core framework
-    https://doi.org/10.1038/s41587-020-0439-x
-* Software dependencies
-    https://github.com/sanger-tol/curationpretext/blob/main/CITATIONS.md
-"""
+//         beforeText = """
+// -\033[2m----------------------------------------------------\033[0m-
+// \033[0;34m   _____                               \033[0;32m _______   \033[0;31m _\033[0m
+// \033[0;34m  / ____|                              \033[0;32m|__   __|  \033[0;31m| |\033[0m
+// \033[0;34m | (___   __ _ _ __   __ _  ___ _ __ \033[0m ___ \033[0;32m| |\033[0;33m ___ \033[0;31m| |\033[0m
+// \033[0;34m  \\___ \\ / _` | '_ \\ / _` |/ _ \\ '__|\033[0m|___|\033[0;32m| |\033[0;33m/ _ \\\033[0;31m| |\033[0m
+// \033[0;34m  ____) | (_| | | | | (_| |  __/ |        \033[0;32m| |\033[0;33m (_) \033[0;31m| |____\033[0m
+// \033[0;34m |_____/ \\__,_|_| |_|\\__, |\\___|_|        \033[0;32m|_|\033[0;33m\\___/\033[0;31m|______|\033[0m
+// \033[0;34m                      __/ |\033[0m
+// \033[0;34m                     |___/\033[0m
+// \033[0;35m  ${manifest.name} ${manifest.version}\033[0m
+// -\033[2m----------------------------------------------------\033[0m-
+// """
+//     afterText = """${manifest.doi ? "\n* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "    https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
+// * The nf-core framework
+//     https://doi.org/10.1038/s41587-020-0439-x
+// * Software dependencies
+//     https://github.com/sanger-tol/curationpretext/blob/main/CITATIONS.md
+// """
     }
 
-    summary {
-        beforeText = validation.help.beforeText
-        afterText = validation.help.afterText
-    }
+    // summary {
+    //     beforeText = validation.help.beforeText
+    //     afterText = validation.help.afterText
+    // }
 }
 
 // Load modules.config for DSL2 module specific options

subworkflows/local/accessory_files/main.nf

@@ -19,8 +19,8 @@ workflow ACCESSORY_FILES {
 
 
     main:
-    ch_versions         = Channel.empty()
-    ch_empty_file       = Channel.fromPath("${baseDir}/assets/EMPTY.txt")
+    ch_versions         = channel.empty()
+    ch_empty_file       = channel.fromPath("${baseDir}/assets/EMPTY.txt")
 
     //
     // NOTE: THIS IS DUPLICATED IN THE CURATIONPRETEXT WORKFLOW,

subworkflows/local/gap_finder/main.nf

@@ -11,7 +11,7 @@ workflow GAP_FINDER {
     reference_tuple     // Channel [ val(meta), path(fasta) ]
 
     main:
-    ch_versions     = Channel.empty()
+    ch_versions     = channel.empty()
 
     //
     // MODULE: GENERATES A GAP SUMMARY FILE

subworkflows/local/generate_maps/main.nf

@@ -20,7 +20,7 @@ workflow GENERATE_MAPS {
 
 
     main:
-    ch_versions             = Channel.empty()
+    ch_versions             = channel.empty()
 
     //
     // MODULE: generate a cram csv file containing the required parametres for CRAM_FILTER_ALIGN_BWAMEM2_FIXMATE_SORT
@@ -80,7 +80,7 @@ workflow GENERATE_MAPS {
         hires_pretext           = PRETEXTMAP_HIGHRES.out.pretext
         ch_versions             = ch_versions.mix( PRETEXTMAP_HIGHRES.out.versions )
     } else {
-        hires_pretext           = Channel.empty()
+        hires_pretext           = channel.empty()
     }
 
     //

subworkflows/local/hic_bwamem2/main.nf

@@ -19,8 +19,7 @@ workflow HIC_BWAMEM2 {
     reference_index     // Channel: tuple [ val(meta), path( fai ) ]
 
     main:
-    ch_versions             = Channel.empty()
-    mappedbam_ch            = Channel.empty()
+    ch_versions             = channel.empty()
 
     //
     // MODULE: Indexing on reference output the folder of indexing files

subworkflows/local/hic_minimap2/main.nf

@@ -21,8 +21,8 @@ workflow HIC_MINIMAP2 {
     reference_index
 
     main:
-    ch_versions         = Channel.empty()
-    mappedbam_ch        = Channel.empty()
+    ch_versions         = channel.empty()
+    mappedbam_ch        = channel.empty()
 
 
     //

subworkflows/local/longread_coverage/main.nf

@@ -17,12 +17,12 @@ workflow LONGREAD_COVERAGE {
 
     take:
     reference_tuple     // Channel: [ val(meta), path( reference_file ) ]
-    reference_index     // Channel: [ val(meta), path( reference_indx ) ]
+    _reference_index    // Channel: [ val(meta), path( reference_indx ) ]
     dot_genome          // Channel: [ val(meta), [  path( datafile )  ] ]
     reads_path          // Channel: [ val(meta),       path( str )      ]
 
     main:
-    ch_versions             = Channel.empty()
+    ch_versions             = channel.empty()
 
     //
     // LOGIC: TAKE THE READ FOLDER AS INPUT AND GENERATE THE CHANNEL OF READ FILES
@@ -107,7 +107,7 @@ workflow LONGREAD_COVERAGE {
     //
     BEDTOOLS_BAMTOBED.out.bed
         .combine( dot_genome )
-        .multiMap { meta, file, my_genome_meta, my_genome ->
+        .multiMap { meta, file, _my_genome_meta, my_genome ->
             input_tuple         :   tuple (
                                         [   id          :   meta.id,
                                             single_end  :   true    ],
@@ -147,7 +147,7 @@ workflow LONGREAD_COVERAGE {
     GNU_SORT.out.sorted
         .combine( dot_genome )
         .combine( reference_tuple )
-        .multiMap { meta, file, meta_my_genome, my_genome, ref_meta, ref ->
+        .multiMap { _meta, file, _meta_my_genome, my_genome, ref_meta, _ref ->
             ch_coverage_bed :   tuple (
                                     [   id: ref_meta.id,
                                         single_end: true

subworkflows/local/repeat_density/main.nf

@@ -24,7 +24,7 @@ workflow REPEAT_DENSITY {
     dot_genome
 
     main:
-    ch_versions         = Channel.empty()
+    ch_versions         = channel.empty()
 
 
     //
@@ -156,7 +156,7 @@ workflow REPEAT_DENSITY {
     //
     UCSC_BEDGRAPHTOBIGWIG(
         GAWK_REPLACE_DOTS.out.output,
-        GNU_SORT_B.out.sorted.map { it[1] }
+        GNU_SORT_B.out.sorted.map { _meta, file -> file }
     )
     ch_versions         = ch_versions.mix( UCSC_BEDGRAPHTOBIGWIG.out.versions )
 

subworkflows/local/telo_extraction/main.nf

@@ -6,7 +6,7 @@ workflow TELO_EXTRACTION {
     telomere_file //tuple(meta, file)
 
     main:
-    ch_versions         = Channel.empty()
+    ch_versions         = channel.empty()
 
     //
     // MODULE: GENERATES A WINDOWS FILE FROM THE ABOVE
@@ -18,7 +18,7 @@ workflow TELO_EXTRACTION {
 
 
     def windows_file    = FIND_TELOMERE_WINDOWS.out.windows
-    def safe_windows    = windows_file.ifEmpty { Channel.empty() }
+    def safe_windows    = windows_file.ifEmpty { channel.empty() }
 
     //
     // MODULE: Extract the telomere data from the FIND_TELOMERE

subworkflows/local/telo_finder/main.nf

@@ -15,7 +15,7 @@ workflow TELO_FINDER {
     teloseq
 
     main:
-    ch_versions     = Channel.empty()
+    ch_versions     = channel.empty()
 
 
     //

subworkflows/local/utils_nfcore_curationpretext_pipeline/main.nf

@@ -79,13 +79,13 @@ workflow PIPELINE_INITIALISATION {
     // Create channel from input file provided through params.input
     //
 
-    input_fasta     = Channel.fromPath(
+    input_fasta     = channel.fromPath(
                         params.input,
                         checkIfExists: true,
                         type: 'file'
                     )
 
-    cram_dir        = Channel.fromPath(
+    cram_dir        = channel.fromPath(
                         params.cram,
                         checkIfExists: true,
                         type: 'dir'
@@ -117,21 +117,21 @@ workflow PIPELINE_INITIALISATION {
         )
     }
 
-    ch_reads        = Channel
-                        .fromPath(
-                            params.reads,
-                            checkIfExists: true,
-                            type: 'dir'
-                        )
-                        .map { dir ->
-                            tuple(
-                                [   id: params.sample,
-                                    single_end: true,
-                                    read_type: params.read_type
-                                ],
-                                dir
-                            )
-                        }
+    channel.fromPath(
+        params.reads,
+        checkIfExists: true,
+        type: 'dir'
+    )
+    .map { dir ->
+        tuple(
+            [   id: params.sample,
+                single_end: true,
+                read_type: params.read_type
+            ],
+            dir
+        )
+    }
+    .set { ch_reads }
 
     emit:
     ch_reference