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feat(merquryfk): version topics and bump to 1.2 (#9734)
feat(merquryfk): version topics and bump to 1.2 (except for ploidyplot which is deprecated in this version)
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-374
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13 files changed

+453
-374
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‎modules/nf-core/merquryfk/katcomp/environment.yml‎

Lines changed: 6 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,9 +1,13 @@
1+
---
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# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
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channels:
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- conda-forge
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- bioconda
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dependencies:
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- bioconda::fastk=1.1.0
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- bioconda::merquryfk=1.1.1
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- bioconda::fastk=1.2
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- bioconda::merquryfk=1.2
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- conda-forge::r-argparse=2.2.3
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- conda-forge::r-cowplot=1.1.3
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- conda-forge::r-ggplot2=3.4.0
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- conda-forge::r-viridis=0.6.5

‎modules/nf-core/merquryfk/katcomp/main.nf‎

Lines changed: 8 additions & 29 deletions
Original file line numberDiff line numberDiff line change
@@ -5,17 +5,19 @@ process MERQURYFK_KATCOMP {
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// WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
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conda "${moduleDir}/environment.yml"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
8-
'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9f/9f0bee9bfacd05665a9b1a11dd087dbf1be41ac3e640931c38c914a2390642cf/data' :
9-
'community.wave.seqera.io/library/fastk_merquryfk_r-cowplot_r-ggplot2_r-viridis:f9994edc2270683c' }"
8+
'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/3f/3fefda33017e34e77a61dd82f8a2884414cdcb222269d9ca72a543bfeb4604b6/data' :
9+
'community.wave.seqera.io/library/fastk_merquryfk_r-argparse_r-cowplot_pruned:d61b120497d4185b' }"
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input:
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tuple val(meta), path(fastk1_hist), path(fastk1_ktab), path(fastk2_hist), path(fastk2_ktab)
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output:
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tuple val(meta), path("*.fi.{png,pdf}"), emit: filled , optional: true
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tuple val(meta), path("*.ln.{png,pdf}"), emit: line , optional: true
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tuple val(meta), path("*.st.{png,pdf}"), emit: stacked, optional: true
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path "versions.yml" , emit: versions
15+
tuple val(meta), path("*.{png,pdf}"), emit: images
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// WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
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tuple val("${task.process}"), val('merquryfk'), eval('echo 1.2'), emit: versions_merquryfk, topic: versions
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// WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
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tuple val("${task.process}"), val('fastk'), eval('echo 1.2'), emit: versions_fastk, topic: versions
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tuple val("${task.process}"), val('R'), eval('R --version | sed "1!d; s/.*version //; s/ .*//"'), emit: versions_r, topic: versions
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2022
when:
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task.ext.when == null || task.ext.when
@@ -25,45 +27,22 @@ process MERQURYFK_KATCOMP {
2527
def prefix = task.ext.prefix ?: "${meta.id}"
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def input_fk1 = fastk1_ktab.find{ it.toString().endsWith(".ktab") }.getBaseName()
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def input_fk2 = fastk2_ktab.find{ it.toString().endsWith(".ktab") }.getBaseName()
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29-
// WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
30-
def FASTK_VERSION = '1.1.0'
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// WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
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def MERQURY_VERSION = '1.1.1'
3330
"""
3431
KatComp \\
3532
$args \\
3633
-T$task.cpus \\
3734
${input_fk1} \\
3835
${input_fk2} \\
3936
$prefix
40-
41-
cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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fastk: $FASTK_VERSION
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merquryfk: $MERQURY_VERSION
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r: \$( R --version | sed '1!d; s/.*version //; s/ .*//' )
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END_VERSIONS
4737
"""
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stub:
5040
def args = task.ext.args ?: ''
5141
def prefix = task.ext.prefix ?: "${meta.id}"
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// WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
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def FASTK_VERSION = '1.1.0'
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// WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
55-
def MERQURY_VERSION = '1.1.1'
5642
def outfmt = args.contains('-pdf') ? "pdf" : "png"
5743
"""
5844
touch ${prefix}.test.fi.${outfmt}
5945
touch ${prefix}.test.ln.${outfmt}
6046
touch ${prefix}.test.st.${outfmt}
61-
62-
cat <<-END_VERSIONS > versions.yml
63-
"${task.process}":
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fastk: $FASTK_VERSION
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merquryfk: $MERQURY_VERSION
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r: \$( R --version | sed '1!d; s/.*version //; s/ .*//' )
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END_VERSIONS
6847
"""
6948
}

‎modules/nf-core/merquryfk/katcomp/meta.yml‎

Lines changed: 62 additions & 36 deletions
Original file line numberDiff line numberDiff line change
@@ -38,52 +38,78 @@ input:
3838
pattern: "*.ktab*"
3939
ontologies: []
4040
output:
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filled:
41+
images:
4242
- - meta:
4343
type: map
4444
description: |
4545
Groovy Map containing sample information
4646
e.g. [ id:'test', single_end:false ]
4747
pattern: "*.fi.{png,pdf}"
48-
- "*.fi.{png,pdf}":
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- "*.{png,pdf}":
4949
type: file
5050
description: |
51-
Comparison of Kmers between sample 1 and 2 in filled PNG or PDF format.
52-
pattern: "*.fi.{png,pdf}"
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ontologies: []
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line:
55-
- - meta:
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type: map
57-
description: |
58-
Groovy Map containing sample information
59-
e.g. [ id:'test', single_end:false ]
60-
pattern: "*.fi.{png,pdf}"
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- "*.ln.{png,pdf}":
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type: file
63-
description: |
64-
Comparison of Kmers between sample 1 and 2 in line PNG or PDF format.
65-
pattern: "*.ln.{png,pdf}"
66-
ontologies: []
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stacked:
68-
- - meta:
69-
type: map
70-
description: |
71-
Groovy Map containing sample information
72-
e.g. [ id:'test', single_end:false ]
73-
pattern: "*.fi.{png,pdf}"
74-
- "*.st.{png,pdf}":
75-
type: file
76-
description: |
77-
Comparison of Kmers between sample 1 and 2 in stacked PNG or PDF format.
78-
pattern: "*.st.{png,pdf}"
51+
Comparison of Kmers between sample 1 and 2 in PNG or PDF format.
52+
pattern: "*.{png,pdf}"
7953
ontologies: []
54+
versions_merquryfk:
55+
- - ${task.process}:
56+
type: string
57+
description: The name of the process
58+
- merquryfk:
59+
type: string
60+
description: The name of the tool
61+
- echo 1.2:
62+
type: eval
63+
description: The expression to obtain the version of the tool
64+
versions_fastk:
65+
- - ${task.process}:
66+
type: string
67+
description: The name of the process
68+
- fastk:
69+
type: string
70+
description: The name of the tool
71+
- echo 1.2:
72+
type: eval
73+
description: The expression to obtain the version of the tool
74+
versions_r:
75+
- - ${task.process}:
76+
type: string
77+
description: The name of the process
78+
- R:
79+
type: string
80+
description: The name of the tool
81+
- R --version | sed "1!d; s/.*version //; s/ .*//":
82+
type: eval
83+
description: The expression to obtain the version of the tool
84+
topics:
8085
versions:
81-
- versions.yml:
82-
type: file
83-
description: File containing software versions
84-
pattern: "versions.yml"
85-
ontologies:
86-
- edam: http://edamontology.org/format_3750 # YAML
86+
- - ${task.process}:
87+
type: string
88+
description: The name of the process
89+
- merquryfk:
90+
type: string
91+
description: The name of the tool
92+
- echo 1.2:
93+
type: eval
94+
description: The expression to obtain the version of the tool
95+
- - ${task.process}:
96+
type: string
97+
description: The name of the process
98+
- fastk:
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type: string
100+
description: The name of the tool
101+
- echo 1.2:
102+
type: eval
103+
description: The expression to obtain the version of the tool
104+
- - ${task.process}:
105+
type: string
106+
description: The name of the process
107+
- R:
108+
type: string
109+
description: The name of the tool
110+
- R --version | sed "1!d; s/.*version //; s/ .*//":
111+
type: eval
112+
description: The expression to obtain the version of the tool
87113
authors:
88114
- "@mahesh-panchal"
89115
maintainers:

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