Generate genome update

assets/schema_input.json

@@ -13,7 +13,14 @@
                     "errorMessage": "Assembly level must be provided"
                 },
                 "assem_version": {
-                    "anyOf": [{ "type": "string" }, { "type": "integer" }],
+                    "anyOf": [
+                        {
+                            "type": "string"
+                        },
+                        {
+                            "type": "integer"
+                        }
+                    ],
                     "errorMessage": "Assembly version must be provided"
                 },
                 "sample_id": {
@@ -41,15 +48,24 @@
         },
         "map_order": {
             "type": "string",
-            "errorMessage": "Map order"
+            "errorMessage": "Map order",
+            "enum": [
+                "length",
+                "unsorted"
+            ]
         },
         "assem_reads": {
             "type": "object",
             "properties": {
                 "read_type": {
                     "type": "string",
                     "errorMessage": "Long read data type",
-                    "enum": ["hifi", "clr", "ont", "illumina"]
+                    "enum": [
+                        "hifi",
+                        "clr",
+                        "ont",
+                        "illumina"
+                    ]
                 },
                 "read_data": {
                     "type": "array",
@@ -77,7 +93,10 @@
                 "hic_aligner": {
                     "type": "string",
                     "errorMessage": "HiC Aligner - minimap2 (default), bwamem2",
-                    "enum": ["minimap2", "bwamem2"]
+                    "enum": [
+                        "minimap2",
+                        "bwamem2"
+                    ]
                 }
             }
         },

modules/local/assign/ancestral/main.nf

@@ -1,5 +1,5 @@
 process ASSIGN_ANCESTRAL {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_low'
 
     conda "conda-forge::python=3.9"

modules/local/bamtobed/sort/main.nf

@@ -1,5 +1,5 @@
 process BAMTOBED_SORT {
-    tag "$meta.id"
+    tag "${meta.id}"
     label "process_high"
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

modules/local/cram/filter_align_bwamem2_fixmate_sort/main.nf

@@ -1,5 +1,5 @@
 process CRAM_FILTER_ALIGN_BWAMEM2_FIXMATE_SORT {
-    tag "$meta.id"
+    tag "${meta.id}"
     label "process_high"
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

modules/local/cram/filter_minimap2_filter5end_fixmate_sort/main.nf

@@ -1,5 +1,5 @@
 process CRAM_FILTER_MINIMAP2_FILTER5END_FIXMATE_SORT {
-    tag "$meta.id"
+    tag "${meta.id}"
     label "process_high"
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

modules/local/extract/ancestral/main.nf

@@ -1,5 +1,5 @@
 process EXTRACT_ANCESTRAL {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_low'
 
     conda "conda-forge::python=3.9"

modules/local/extract/repeat/main.nf

@@ -1,5 +1,5 @@
 process EXTRACT_REPEAT {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_low'
 
     conda "conda-forge::perl=5.26.2"
@@ -8,38 +8,25 @@ process EXTRACT_REPEAT {
         'biocontainers/perl:5.26.2' }"
 
     input:
-    tuple val( meta ), path( file )
+    tuple val(meta), path(file)
 
     output:
     tuple val( meta ), path( "*.bed" )  , emit: bed
-    path "versions.yml"                 , emit: versions
+    tuple val("${task.process}"), val('extract_repeat.pl'), val("1.0.0"), topic: versions, emit: versions_extractrepeat
+    tuple val("${task.process}"), val('perl'), eval("perl --version | sed -n 's/.*(v\\([0-9.]\\+\\)).*/\\1/p'"), topic: versions, emit: versions_perl
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    def prefix      = task.ext.prefix ?: "${meta.id}"
-    def VERSION     = "1.0" // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    def prefix = task.ext.prefix ?: "${meta.id}"
     """
     extract_repeat.pl $file > ${prefix}_repeats.bed
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        perl: \$(echo \$(perl --version 2>&1) | sed 's/^.*perl //; s/Using.*\$//')
-        extract_repeat.pl: $VERSION
-    END_VERSIONS
     """
 
     stub:
-    def prefix      = task.ext.prefix ?: "${meta.id}"
-    def VERSION     = "1.0" // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    def prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}_repeats.bed
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        perl: \$(echo \$(perl --version 2>&1) | sed 's/^.*perl //; s/Using.*\$//')
-        extract_repeat.pl: $VERSION
-    END_VERSIONS
     """
 }

modules/local/find/half_coverage/main.nf

@@ -14,7 +14,8 @@ process FIND_HALF_COVERAGE {
 
     output:
     tuple val(meta), path("*.bed")  , emit: bed
-    path "versions.yml"             , emit: versions
+    tuple val("${task.process}"), val('findHalfcoverage.py'), eval("findHalfcoverage.py --version | sed 's/^.*.py //'"), topic: versions, emit: versions_findhalfcoverage
+    tuple val("${task.process}"), val('python'), eval("python --version | sed 's/^Python //'"), topic: versions, emit: versions_python
 
     when:
     task.ext.when == null || task.ext.when
@@ -23,23 +24,11 @@ process FIND_HALF_COVERAGE {
     def prefix  = task.ext.prefix   ?: "halfcoverage"
     """
     findHalfcoverage.py -c $bedfile -m $my_genome -d $depthgraph > ${prefix}.bed
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        python: \$(echo \$(python --version 2>&1) | sed 's/^.*python //; s/Using.*\$//')
-        findHalfcoverage.py: \$(findHalfcoverage.py --version | cut -d' ' -f2)
-    END_VERSIONS
     """
 
     stub:
     def prefix = task.ext.prefix ?: "halfcoverage"
     """
     touch ${prefix}.bed
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        python: \$(echo \$(python --version 2>&1) | sed 's/^.*python //; s/Using.*\$//')
-        findHalfcoverage.py: \$(findHalfcoverage.py --version | cut -d' ' -f2)
-    END_VERSIONS
     """
 }

modules/local/get/paired_contact_bed/main.nf

@@ -1,5 +1,5 @@
 process GET_PAIRED_CONTACT_BED {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_low'
 
     conda "conda-forge::coreutils=9.1"

modules/local/graph/overall_coverage/main.nf

@@ -1,5 +1,5 @@
 process GRAPH_OVERALL_COVERAGE {
-    tag "$meta.id"
+    tag "${meta.id}"
     label "process_single"
 
     conda "conda-forge::perl=5.26.2"
@@ -12,7 +12,8 @@ process GRAPH_OVERALL_COVERAGE {
 
     output:
     tuple val(meta), path("*.part") , emit: part
-    path "versions.yml"             , emit: versions
+    tuple val("${task.process}"), val('graph_overall_coverage.pl'), eval("graph_overall_coverage.pl --version"), topic: versions, emit: versions_graph_overall_coverage
+    tuple val("${task.process}"), val('perl'), eval("perl --version | sed -n 's/.*(v\\([0-9.]\\+\\)).*/\\1/p'"), topic: versions, emit: versions_perl
 
     when:
     task.ext.when == null || task.ext.when
@@ -21,23 +22,11 @@ process GRAPH_OVERALL_COVERAGE {
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     graph_overall_coverage.pl $bed > ${prefix}.part
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        perl: \$(echo \$(perl --version 2>&1) | sed 's/^.*perl //; s/Using.*\$//')
-        graph_overall_coverage.pl: \$(graph_overall_coverage.pl --version)
-    END_VERSIONS
     """
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}.part
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        perl: \$(echo \$(perl --version 2>&1) | sed 's/^.*perl //; s/Using.*\$//')
-        graph_overall_coverage.pl: \$(graph_overall_coverage.pl --version)
-    END_VERSIONS
     """
 }

modules/local/makecmap/cmap2bed/main.nf

@@ -1,5 +1,5 @@
 process MAKECMAP_CMAP2BED {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_single'
 
     conda "conda-forge::python=3.9"
@@ -13,7 +13,8 @@ process MAKECMAP_CMAP2BED {
 
     output:
     tuple val(meta), path("*.bed"), emit: bedfile
-    path "versions.yml"           , emit: versions
+    tuple val("${task.process}"), val('cmap2bed.py'), eval("cmap2bed.py --version | sed 's/^.*.py //'"), topic: versions, emit: versions_cmap2bed
+    tuple val("${task.process}"), val('python'), eval("python --version | sed 's/^Python //'"), topic: versions, emit: versions_python
 
     when:
     task.ext.when == null || task.ext.when
@@ -23,23 +24,11 @@ process MAKECMAP_CMAP2BED {
     """
     grep -v '#' $cmap > ${prefix}_${enzyme}_edited.cmap
     cmap2bed.py -t ${prefix}_${enzyme}_edited.cmap -z $enzyme | sort -k1,1 -k2,2n > ${enzyme}.bed
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        python: \$(echo \$(python --version 2>&1) | sed 's/^.*python //; s/Using.*\$//')
-        cmap2bed.py: \$(cmap2bed.py --version | cut -d' ' -f2)
-    END_VERSIONS
     """
 
     stub:
     def prefix  = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}_${enzyme}.bed
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        python: \$(echo \$(python --version 2>&1) | sed 's/^.*python //; s/Using.*\$//')
-        cmap2bed.py: \$(cmap2bed.py --version | cut -d' ' -f2)
-    END_VERSIONS
     """
 }

modules/local/makecmap/fa2cmapmulticolor/main.nf

@@ -1,5 +1,5 @@
 process MAKECMAP_FA2CMAPMULTICOLOR {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_low'
 
     conda "conda-forge::perl=5.26.2"
@@ -14,7 +14,8 @@ process MAKECMAP_FA2CMAPMULTICOLOR {
     output:
     tuple val(meta), path("*.cmap"), emit: cmap
     path("*key.txt")               , emit: cmapkey
-    path "versions.yml"            , emit: versions
+    tuple val("${task.process}"), val('fa2cmap_multi_color.pl'), eval("fa2cmap_multi_color.pl -v"), topic: versions, emit: versions_fa2cmap_multi_color
+    tuple val("${task.process}"), val('perl'), eval("perl --version | sed -n 's/.*(v\\([0-9.]\\+\\)).*/\\1/p'"), topic: versions, emit: versions_perl
 
     when:
     task.ext.when == null || task.ext.when
@@ -23,22 +24,10 @@ process MAKECMAP_FA2CMAPMULTICOLOR {
     def args    = task.ext.args ?: ''
     """
     fa2cmap_multi_color.pl -i $fasta -e $enzyme 1 $args
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        perl: \$(echo \$(perl --version 2>&1) | sed 's/^.*perl //; s/Using.*\$//')
-        fa2cmap_multi_color.pl: \$(fa2cmap_multi_color.pl -v)
-    END_VERSIONS
     """
 
     stub:
     """
     touch ${enzyme}_key.cmap
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        perl: \$(echo \$(perl --version 2>&1) | sed 's/^.*perl //; s/Using.*\$//')
-        fa2cmap_multi_color.pl: \$(fa2cmap_multi_color.pl -v)
-    END_VERSIONS
     """
 }

modules/local/makecmap/renamecmapids/main.nf

@@ -1,5 +1,5 @@
 process MAKECMAP_RENAMECMAPIDS {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_low'
 
     conda "conda-forge::perl=5.26.2"
@@ -13,7 +13,8 @@ process MAKECMAP_RENAMECMAPIDS {
 
     output:
     tuple val(meta), path("*.cmap"), emit: renamedcmap
-    path "versions.yml"            , emit: versions
+    tuple val("${task.process}"), val('rename_cmapids.pl'), eval("rename_cmapids.pl -version"), topic: versions, emit: versions_renamedcmap
+    tuple val("${task.process}"), val('perl'), eval("perl --version | sed -n 's/.*(v\\([0-9.]\\+\\)).*/\\1/p'"), topic: versions, emit: versions_perl
 
     when:
     task.ext.when == null || task.ext.when
@@ -24,23 +25,11 @@ process MAKECMAP_RENAMECMAPIDS {
 
     """
     rename_cmapids.pl -cmapfile $cmap -idx_key $keys $args > ${prefix}_EDITED.cmap
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        perl: \$(echo \$(perl --version 2>&1) | sed 's/^.*perl //; s/Using.*\$//')
-        rename_cmapids.pl: \$(rename_cmapids.pl -version)
-    END_VERSIONS
     """
 
     stub:
     def prefix  = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}_EDITED.cmap
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        perl: \$(echo \$(perl --version 2>&1) | sed 's/^.*perl //; s/Using.*\$//')
-        rename_cmapids.pl: \$(rename_cmapids.pl -version)
-    END_VERSIONS
     """
 }

modules/local/pretext/graph/main.nf

@@ -1,5 +1,5 @@
 process PRETEXT_GRAPH {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_single'
 
     container "quay.io/sanger-tol/pretext:0.0.9-yy5-c2"

modules/local/selfcomp/alignmentblocks/main.nf

@@ -1,5 +1,5 @@
 process SELFCOMP_ALIGNMENTBLOCKS {
-    tag "$meta.id"
+    tag "${meta.id}"
     label "process_medium"
 
     conda "conda-forge::python=3.9"
@@ -25,7 +25,7 @@ process SELFCOMP_ALIGNMENTBLOCKS {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        python: \$(echo \$(python --version 2>&1) | sed 's/^.*python //; s/Using.*\$//')
+        python: \$(echo \$(python --version 2>&1) | sed 's/^Python //')
         pandas: \$(echo \$(pandas: python -c "import pandas as pd; print(pd.__version__)"))
         pybedtools: \$(echo \$(pybedtools: python -c "import pybedtools as pb; print(pb.__version__)"))
         build_alignment_block.py: \$(build_alignment_block.py --version | cut -d' ' -f2)

modules/local/selfcomp/mapids/main.nf

@@ -1,5 +1,5 @@
 process SELFCOMP_MAPIDS {
-    tag "$meta.id"
+    tag "${meta.id}"
     label "process_medium"
 
     conda "conda-forge::python=3.9"
@@ -25,7 +25,7 @@ process SELFCOMP_MAPIDS {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        python: \$(echo \$(python --version 2>&1) | sed 's/^.*python //; s/Using.*\$//')
+        python: \$(echo \$(python --version 2>&1) | sed 's/^Python //')
         mapids.py: \$(mapids.py --version | cut -d' ' -f2)
     END_VERSIONS
     """