Build branch demultiplex/v0.6 with version v0.6.4 to demultiplex on branch v0.6 (dc228b2)
Build pipeline: viash-hub.demultiplex.v0.6.4-w8bvk
Source commit: dc228b2b4e
Source message: Bump version to v0.6.4
This commit is contained in:
@@ -1,3 +1,11 @@
|
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# demultiplex v0.6.4
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|
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## Minor changes
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* Replace FastQC by Falco again, Falco is now able to handle empty FASTQ files (PR #71, PR #73).
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* Improve publishing speed by keeping symbolic links (PR #72).
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# demultiplex v0.6.3
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|
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## Bug fixes
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@@ -1,5 +1,5 @@
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name: demultiplex
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version: v0.6.3
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version: v0.6.4
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description: |
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Demultiplexing pipeline
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license: MIT
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@@ -96,7 +96,7 @@ dependencies:
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repository: bb
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- name: bases2fastq
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repository: bb
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- name: fastqc
|
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- name: falco
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repository: bb
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- name: multiqc
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repository: bb
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|
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@@ -113,25 +113,35 @@ workflow run_wf {
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],
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)
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output_ch = samples_ch
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| fastqc.run(
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output_ch = samples_ch
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| falco.run(
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directives: [label: ["lowcpu", "midmem"]],
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fromState: {id, state ->
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def output_base = "$id/qc/fastqc/*"
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[
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"input": [state.fastq_forward, state.fastq_reverse],
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"html": "${output_base}_fastqc_report.html",
|
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"summary": "${output_base}_summary.txt",
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"data": "${output_base}_fastqc_data.txt",
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def input = state.fastq_forward + state.fastq_reverse
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||||
def state_mapping = [
|
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"input": input,
|
||||
"outdir": "$id/qc/falco",
|
||||
"summary_filename": null,
|
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"report_filename": null,
|
||||
"data_filename": null,
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||||
"allow_empty_input": true
|
||||
]
|
||||
// When a single FASTQ is being processed, Falco does not automatically
|
||||
// determine the basename from the input file. But this can be done manually here.
|
||||
if (input.size() == 1) {
|
||||
def basename = input[0].name
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||||
state_mapping += [
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"summary_filename": "$id/qc/falco/${basename}_summary.txt",
|
||||
"report_filename": "$id/qc/falco/${basename}_fastqc_report.html",
|
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"data_filename": "$id/qc/falco/${basename}_fastqc_data.txt"
|
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]
|
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}
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return state_mapping
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},
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toState: { id, result, state ->
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// The output directory for all files above is the same:
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// take the directory from one of the files
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state + [ "output_sample_qc": result.html[0].parent ]
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state + [ "output_sample_qc" : result.outdir ]
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||||
}
|
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)
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|
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| combine_samples.run(
|
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fromState: { id, state ->
|
||||
[
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||||
|
||||
@@ -19,7 +19,7 @@ do
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mkdir -p $(dirname "$output_location") && echo "Containing directory $output_location created"
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|
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echo "Copying files..."
|
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cp -rL "$input_location" "$output_location"
|
||||
cp -a --keep-directory-symlink "$input_location" "$output_location"
|
||||
|
||||
echo "Output files for $output_location:"
|
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ls "$output_location"
|
||||
@@ -30,5 +30,5 @@ mkdir -p "$par_output_sample_qc"
|
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IFS=";" read -ra sample_qc_inputs <<< $par_input_sample_qc
|
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for qc_dir in "${sample_qc_inputs[@]}"; do
|
||||
echo "Copying contents of $qc_dir"
|
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find -H -D exec "$qc_dir" -type f -maxdepth 1 -exec cp -t "$par_output_sample_qc" {} +
|
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find -H -D exec "$qc_dir" -type f -maxdepth 1 -exec cp -a --keep-directory-symlink -t "$par_output_sample_qc" {} +
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||||
done
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@@ -76,21 +76,21 @@ workflow test {
|
||||
assert published_items.collect{it.name}.toSet() == ["demultiplexer_logs", "fastq", "qc", "SampleSheet.csv", "transfer_completed.txt"].toSet()
|
||||
def fastqc_files = publish_dir.resolve("qc/fastqc").listFiles()
|
||||
assert fastqc_files.collect{it.name}.toSet() == [
|
||||
"Sample1_S1_L001_R1_001_fastqc_data.txt",
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||||
"Sample1_S1_L001_R1_001_fastqc_report.html",
|
||||
"Sample1_S1_L001_R1_001_summary.txt",
|
||||
"Sample23_S3_L001_R1_001_fastqc_data.txt",
|
||||
"Sample23_S3_L001_R1_001_fastqc_report.html",
|
||||
"Sample23_S3_L001_R1_001_summary.txt",
|
||||
"SampleA_S2_L001_R1_001_fastqc_data.txt",
|
||||
"SampleA_S2_L001_R1_001_fastqc_report.html",
|
||||
"SampleA_S2_L001_R1_001_summary.txt",
|
||||
"sampletest_S4_L001_R1_001_fastqc_data.txt",
|
||||
"sampletest_S4_L001_R1_001_fastqc_report.html",
|
||||
"sampletest_S4_L001_R1_001_summary.txt",
|
||||
"Undetermined_S0_L001_R1_001_fastqc_data.txt",
|
||||
"Undetermined_S0_L001_R1_001_fastqc_report.html",
|
||||
"Undetermined_S0_L001_R1_001_summary.txt"
|
||||
"Sample1_S1_L001_R1_001.fastq.gz_fastqc_data.txt",
|
||||
"Sample1_S1_L001_R1_001.fastq.gz_fastqc_report.html",
|
||||
"Sample1_S1_L001_R1_001.fastq.gz_summary.txt",
|
||||
"Sample23_S3_L001_R1_001.fastq.gz_fastqc_data.txt",
|
||||
"Sample23_S3_L001_R1_001.fastq.gz_fastqc_report.html",
|
||||
"Sample23_S3_L001_R1_001.fastq.gz_summary.txt",
|
||||
"SampleA_S2_L001_R1_001.fastq.gz_fastqc_data.txt",
|
||||
"SampleA_S2_L001_R1_001.fastq.gz_fastqc_report.html",
|
||||
"SampleA_S2_L001_R1_001.fastq.gz_summary.txt",
|
||||
"sampletest_S4_L001_R1_001.fastq.gz_fastqc_data.txt",
|
||||
"sampletest_S4_L001_R1_001.fastq.gz_fastqc_report.html",
|
||||
"sampletest_S4_L001_R1_001.fastq.gz_summary.txt",
|
||||
"Undetermined_S0_L001_R1_001.fastq.gz_fastqc_data.txt",
|
||||
"Undetermined_S0_L001_R1_001.fastq.gz_fastqc_report.html",
|
||||
"Undetermined_S0_L001_R1_001.fastq.gz_summary.txt"
|
||||
].toSet()
|
||||
assert publish_dir.resolve("qc/multiqc_report.html").exists()
|
||||
def fastq_files = publish_dir.resolve("fastq").listFiles()
|
||||
|
||||
@@ -1,179 +1,49 @@
|
||||
name: "fastqc"
|
||||
name: "falco"
|
||||
version: "v0.4.1"
|
||||
authors:
|
||||
- name: "Theodoro Gasperin Terra Camargo"
|
||||
- name: "Toni Verbeiren"
|
||||
roles:
|
||||
- "author"
|
||||
- "maintainer"
|
||||
info:
|
||||
links:
|
||||
email: "theodorogtc@gmail.com"
|
||||
github: "tgaspe"
|
||||
linkedin: "theodoro-gasperin-terra-camargo"
|
||||
github: "tverbeiren"
|
||||
linkedin: "verbeiren"
|
||||
organizations:
|
||||
- name: "Data Intuitive"
|
||||
href: "https://www.data-intuitive.com"
|
||||
role: "Data Scientist and CEO"
|
||||
argument_groups:
|
||||
- name: "Inputs"
|
||||
- name: "Input arguments"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--input"
|
||||
description: "FASTQ file(s) to be analyzed.\n"
|
||||
description: "input fastq files"
|
||||
info: null
|
||||
example:
|
||||
- "input.fq"
|
||||
- "input1.fastq;input2.fastq"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: true
|
||||
multiple_sep: ";"
|
||||
- name: "Outputs"
|
||||
description: "At least one of the output options (--html, --zip, --summary, --data)\
|
||||
\ must be used.\n"
|
||||
- name: "Run arguments"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--outdir"
|
||||
description: "Output directory where the results will be saved.\n"
|
||||
info: null
|
||||
example:
|
||||
- "results"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--html"
|
||||
description: "Create the HTML report of the results. \n'*' wild card must be provided\
|
||||
\ in the output file name. \nWild card will be replaced by the input file basename.\n\
|
||||
e.g. \n --input \"sample_1.fq\"\n --html \"*.html\"\n would create an output\
|
||||
\ html file named sample_1.html\n"
|
||||
info: null
|
||||
example:
|
||||
- "*.html"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: true
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--zip"
|
||||
description: "Create the zip file(s) containing: html report, data, images, icons,\
|
||||
\ summary, etc.\n'*' wild card must be provided in the output file name.\nWild\
|
||||
\ card will be replaced by the input basename.\ne.g. \n --input \"sample_1.fq\"\
|
||||
\n --html \"*.zip\"\n would create an output zip file named sample_1.zip\n"
|
||||
info: null
|
||||
example:
|
||||
- "*.zip"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: true
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--summary"
|
||||
description: "Create the summary file(s).\n'*' wild card must be provided in the\
|
||||
\ output file name.\nWild card will be replaced by the input basename.\ne.g.\
|
||||
\ \n --input \"sample_1.fq\"\n --summary \"*_summary.txt\"\n would create\
|
||||
\ an output summary.txt file named sample_1_summary.txt\n"
|
||||
info: null
|
||||
example:
|
||||
- "*_summary.txt"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: true
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--data"
|
||||
description: "Create the data file(s).\n'*' wild card must be provided in the\
|
||||
\ output file name.\nWild card will be replaced by the input basename.\ne.g.\
|
||||
\ \n --input \"sample_1.fq\"\n --summary \"*_data.txt\"\n would create an\
|
||||
\ output data.txt file named sample_1_data.txt\n"
|
||||
info: null
|
||||
example:
|
||||
- "*_data.txt"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: true
|
||||
multiple_sep: ";"
|
||||
- name: "Options"
|
||||
arguments:
|
||||
- type: "boolean_true"
|
||||
name: "--casava"
|
||||
description: "Files come from raw casava output. Files in the same sample\ngroup\
|
||||
\ (differing only by the group number) will be analysed\nas a set rather than\
|
||||
\ individually. Sequences with the filter\nflag set in the header will be excluded\
|
||||
\ from the analysis.\nFiles must have the same names given to them by casava\n\
|
||||
(including being gzipped and ending with .gz) otherwise they\nwon't be grouped\
|
||||
\ together correctly.\n"
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "boolean_true"
|
||||
name: "--nano"
|
||||
description: "Files come from nanopore sequences and are in fast5 format. In\n\
|
||||
this mode you can pass in directories to process and the program\nwill take\
|
||||
\ in all fast5 files within those directories and produce\na single output file\
|
||||
\ from the sequences found in all files.\n"
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "boolean_true"
|
||||
name: "--nofilter"
|
||||
description: "If running with --casava then don't remove read flagged by\ncasava\
|
||||
\ as poor quality when performing the QC analysis.\n"
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "boolean_true"
|
||||
name: "--nogroup"
|
||||
description: "Disable grouping of bases for reads >50bp. \nAll reports will show\
|
||||
\ data for every base in the read. \nWARNING: Using this option will cause fastqc\
|
||||
\ to crash \nand burn if you use it on really long reads, and your \nplots may\
|
||||
\ end up a ridiculous size. You have been warned!\n"
|
||||
\ data for every base in \nthe read. WARNING: When using this option, \nyour\
|
||||
\ plots may end up a ridiculous size. You \nhave been warned!\n"
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "integer"
|
||||
name: "--min_length"
|
||||
description: "Sets an artificial lower limit on the length of the \nsequence to\
|
||||
\ be shown in the report. As long as you \nset this to a value greater or equal\
|
||||
\ to your longest \nread length then this will be the sequence length used \n\
|
||||
to create your read groups. This can be useful for making\ndirectly comparable\
|
||||
\ statistics from datasets with somewhat \nvariable read lengths.\n"
|
||||
info: null
|
||||
example:
|
||||
- 0
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--format"
|
||||
alternatives:
|
||||
- "-f"
|
||||
description: "Bypasses the normal sequence file format detection and \nforces\
|
||||
\ the program to use the specified format. \nValid formats are bam, sam, bam_mapped,\
|
||||
\ sam_mapped, and fastq.\n"
|
||||
info: null
|
||||
example:
|
||||
- "bam"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--contaminants"
|
||||
alternatives:
|
||||
- "-c"
|
||||
description: "Specifies a non-default file which contains the list \nof contaminants\
|
||||
\ to screen overrepresented sequences against. \nThe file must contain sets\
|
||||
\ of named contaminants in the form\nname[tab]sequence. Lines prefixed with\
|
||||
\ a hash will be ignored.\n"
|
||||
name: "--contaminents"
|
||||
description: "Specifies a non-default file which contains \nthe list of contaminants\
|
||||
\ to screen \noverrepresented sequences against. The file \nmust contain sets\
|
||||
\ of named contaminants in \nthe form name[tab]sequence. Lines prefixed \nwith\
|
||||
\ a hash will be ignored. Default: \nhttps://github.com/smithlabcode/falco/blob/v1.2.5/Configuration/contaminant_list.txt\n"
|
||||
info: null
|
||||
example:
|
||||
- "contaminants.txt"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
@@ -182,15 +52,11 @@ argument_groups:
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--adapters"
|
||||
alternatives:
|
||||
- "-a"
|
||||
description: "Specifies a non-default file which contains the list of \nadapter\
|
||||
\ sequences which will be explicitly searched against \nthe library. The file\
|
||||
\ must contain sets of named adapters \nin the form name[tab]sequence. Lines\
|
||||
\ prefixed with a hash will be ignored.\n"
|
||||
description: "Specifies a non-default file which contains \nthe list of adapter\
|
||||
\ sequences which will be \nexplicity searched against the library. The \nfile\
|
||||
\ must contain sets of named adapters in \nthe form name[tab]sequence. Lines\
|
||||
\ prefixed \nwith a hash will be ignored. Default:\nhttps://github.com/smithlabcode/falco/blob/v1.2.5/Configuration/adapter_list.txt\n"
|
||||
info: null
|
||||
example:
|
||||
- "adapters.txt"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
@@ -199,16 +65,12 @@ argument_groups:
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--limits"
|
||||
alternatives:
|
||||
- "-l"
|
||||
description: "Specifies a non-default file which contains \na set of criteria\
|
||||
\ which will be used to determine \nthe warn/error limits for the various modules.\
|
||||
\ \nThis file can also be used to selectively remove \nsome modules from the\
|
||||
\ output altogether. The format \nneeds to mirror the default limits.txt file\
|
||||
\ found in \nthe Configuration folder.\n"
|
||||
\ which will be used to \ndetermine the warn/error limits for the \nvarious\
|
||||
\ modules. This file can also be used \nto selectively remove some modules from\
|
||||
\ the \noutput all together. The format needs to \nmirror the default limits.txt\
|
||||
\ file found in \nthe Configuration folder. Default: \nhttps://github.com/smithlabcode/falco/blob/v1.2.5/Configuration/limits.txt\n"
|
||||
info: null
|
||||
example:
|
||||
- "limits.txt"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
@@ -216,35 +78,137 @@ argument_groups:
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--kmers"
|
||||
name: "--subsample"
|
||||
alternatives:
|
||||
- "-k"
|
||||
description: "Specifies the length of Kmer to look for in the Kmer \ncontent module.\
|
||||
\ Specified Kmer length must be between \n2 and 10. Default length is 7 if not\
|
||||
\ specified.\n"
|
||||
- "-s"
|
||||
description: "[Falco only] makes falco faster (but \npossibly less accurate) by\
|
||||
\ only processing \nreads that are a multiple of this value (using \n0-based\
|
||||
\ indexing to number reads).\n"
|
||||
info: null
|
||||
example:
|
||||
- 7
|
||||
- 10
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "boolean_true"
|
||||
name: "--quiet"
|
||||
name: "--bisulfite"
|
||||
alternatives:
|
||||
- "-q"
|
||||
description: "Suppress all progress messages on stdout and only report errors.\n"
|
||||
- "-b"
|
||||
description: "[Falco only] reads are whole genome \nbisulfite sequencing, and\
|
||||
\ more Ts and fewer \nCs are therefore expected and will be \naccounted for\
|
||||
\ in base content.\n"
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "boolean_true"
|
||||
name: "--reverse_complement"
|
||||
alternatives:
|
||||
- "-r"
|
||||
description: "[Falco only] The input is a \nreverse-complement. All modules will\
|
||||
\ be \ntested by swapping A/T and C/G\n"
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "boolean_true"
|
||||
name: "--allow_empty_input"
|
||||
description: "Allow empty input files and generate empty output files without\
|
||||
\ an error state.\n"
|
||||
info: null
|
||||
direction: "input"
|
||||
- name: "Output arguments"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--outdir"
|
||||
alternatives:
|
||||
- "-o"
|
||||
description: "Create all output files in the specified \noutput directory. FALCO-SPECIFIC:\
|
||||
\ If the \ndirectory does not exists, the program will \ncreate it.\n"
|
||||
info: null
|
||||
example:
|
||||
- "output"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--format"
|
||||
alternatives:
|
||||
- "-f"
|
||||
description: "Bypasses the normal sequence file format \ndetection and forces\
|
||||
\ the program to use the \nspecified format. Validformats are bam, sam, \nbam_mapped,\
|
||||
\ sam_mapped, fastq, fq, fastq.gz \nor fq.gz.\n"
|
||||
info: null
|
||||
required: false
|
||||
choices:
|
||||
- "bam"
|
||||
- "sam"
|
||||
- "bam_mapped"
|
||||
- "sam_mapped"
|
||||
- "fastq"
|
||||
- "fq"
|
||||
- "fastq.gz"
|
||||
- "fq.gz"
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--data_filename"
|
||||
alternatives:
|
||||
- "-D"
|
||||
description: "[Falco only] Specify filename for FastQC \ndata output (TXT). If\
|
||||
\ not specified, it will \nbe called fastq_data.txt in either the input \nfile's\
|
||||
\ directory or the one specified in the \n--output flag. Only available when\
|
||||
\ running \nfalco with a single input.\n"
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--report_filename"
|
||||
alternatives:
|
||||
- "-R"
|
||||
description: "[Falco only] Specify filename for FastQC \nreport output (HTML).\
|
||||
\ If not specified, it \nwill be called fastq_report.html in either \nthe input\
|
||||
\ file's directory or the one \nspecified in the --output flag. Only \navailable\
|
||||
\ when running falco with a single \ninput.\n"
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--summary_filename"
|
||||
alternatives:
|
||||
- "-S"
|
||||
description: "[Falco only] Specify filename for the short \nsummary output (TXT).\
|
||||
\ If not specified, it \nwill be called fastq_report.html in either \nthe input\
|
||||
\ file's directory or the one \nspecified in the --output flag. Only \navailable\
|
||||
\ when running falco with a single \ninput.\n"
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
resources:
|
||||
- type: "bash_script"
|
||||
path: "script.sh"
|
||||
is_executable: true
|
||||
description: "FastQC - A high throughput sequence QC analysis tool."
|
||||
description: "A C++ drop-in replacement of FastQC to assess the quality of sequence\
|
||||
\ read data"
|
||||
test_resources:
|
||||
- type: "bash_script"
|
||||
path: "test.sh"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "test_helpers.sh"
|
||||
info: null
|
||||
status: "enabled"
|
||||
scope:
|
||||
@@ -252,18 +216,19 @@ scope:
|
||||
target: "public"
|
||||
requirements:
|
||||
commands:
|
||||
- "falco"
|
||||
- "ps"
|
||||
keywords:
|
||||
- "Quality control"
|
||||
- "BAM"
|
||||
- "SAM"
|
||||
- "FASTQ"
|
||||
license: "GPL-3.0, Apache-2.0"
|
||||
- "qc"
|
||||
- "fastqc"
|
||||
- "sequencing"
|
||||
license: "GPL-3.0"
|
||||
references:
|
||||
doi:
|
||||
- "10.12688/f1000research.21142.2"
|
||||
links:
|
||||
repository: "https://github.com/s-andrews/FastQC"
|
||||
homepage: "https://www.bioinformatics.babraham.ac.uk/projects/fastqc/"
|
||||
documentation: "https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/"
|
||||
issue_tracker: "https://github.com/s-andrews/FastQC/issues"
|
||||
repository: "https://github.com/smithlabcode/falco"
|
||||
documentation: "https://falco.readthedocs.io/en/latest/"
|
||||
runners:
|
||||
- type: "executable"
|
||||
id: "executable"
|
||||
@@ -332,24 +297,24 @@ runners:
|
||||
engines:
|
||||
- type: "docker"
|
||||
id: "docker"
|
||||
image: "biocontainers/fastqc:v0.11.9_cv8"
|
||||
image: "quay.io/biocontainers/falco:1.2.5--h077b44d_0"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "v0.4.1"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "docker"
|
||||
run:
|
||||
- "echo \"fastqc: $(fastqc --version | sed -n 's/^FastQC //p')\" > /var/software_versions.txt\n"
|
||||
- "echo \"falco: \\\"$(falco -v | sed -n 's/^falco //p')\\\"\" > /var/software_versions.txt\n"
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/fastqc/config.vsh.yaml"
|
||||
config: "src/falco/config.vsh.yaml"
|
||||
runner: "nextflow"
|
||||
engine: "docker|native"
|
||||
output: "target/nextflow/fastqc"
|
||||
executable: "target/nextflow/fastqc/main.nf"
|
||||
output: "target/nextflow/falco"
|
||||
executable: "target/nextflow/falco/main.nf"
|
||||
viash_version: "0.9.4"
|
||||
git_commit: "69186bfc6beed075e81e10f17d24c4c999e87484"
|
||||
git_remote: "https://github.com/viash-hub/biobox"
|
||||
@@ -1,4 +1,4 @@
|
||||
// fastqc v0.4.1
|
||||
// falco v0.4.1
|
||||
//
|
||||
// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
|
||||
// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
|
||||
@@ -10,7 +10,7 @@
|
||||
// files.
|
||||
//
|
||||
// Component authors:
|
||||
// * Theodoro Gasperin Terra Camargo (author, maintainer)
|
||||
// * Toni Verbeiren (author, maintainer)
|
||||
|
||||
////////////////////////////
|
||||
// VDSL3 helper functions //
|
||||
@@ -3033,34 +3033,40 @@ nextflow.enable.dsl=2
|
||||
meta = [
|
||||
"resources_dir": moduleDir.toRealPath().normalize(),
|
||||
"config": processConfig(readJsonBlob('''{
|
||||
"name" : "fastqc",
|
||||
"name" : "falco",
|
||||
"version" : "v0.4.1",
|
||||
"authors" : [
|
||||
{
|
||||
"name" : "Theodoro Gasperin Terra Camargo",
|
||||
"name" : "Toni Verbeiren",
|
||||
"roles" : [
|
||||
"author",
|
||||
"maintainer"
|
||||
],
|
||||
"info" : {
|
||||
"links" : {
|
||||
"email" : "theodorogtc@gmail.com",
|
||||
"github" : "tgaspe",
|
||||
"linkedin" : "theodoro-gasperin-terra-camargo"
|
||||
}
|
||||
"github" : "tverbeiren",
|
||||
"linkedin" : "verbeiren"
|
||||
},
|
||||
"organizations" : [
|
||||
{
|
||||
"name" : "Data Intuitive",
|
||||
"href" : "https://www.data-intuitive.com",
|
||||
"role" : "Data Scientist and CEO"
|
||||
}
|
||||
]
|
||||
}
|
||||
}
|
||||
],
|
||||
"argument_groups" : [
|
||||
{
|
||||
"name" : "Inputs",
|
||||
"name" : "Input arguments",
|
||||
"arguments" : [
|
||||
{
|
||||
"type" : "file",
|
||||
"name" : "--input",
|
||||
"description" : "FASTQ file(s) to be analyzed.\n",
|
||||
"description" : "input fastq files",
|
||||
"example" : [
|
||||
"input.fq"
|
||||
"input1.fastq;input2.fastq"
|
||||
],
|
||||
"must_exist" : true,
|
||||
"create_parent" : true,
|
||||
@@ -3072,145 +3078,18 @@ meta = [
|
||||
]
|
||||
},
|
||||
{
|
||||
"name" : "Outputs",
|
||||
"description" : "At least one of the output options (--html, --zip, --summary, --data) must be used.\n",
|
||||
"name" : "Run arguments",
|
||||
"arguments" : [
|
||||
{
|
||||
"type" : "file",
|
||||
"name" : "--outdir",
|
||||
"description" : "Output directory where the results will be saved.\n",
|
||||
"example" : [
|
||||
"results"
|
||||
],
|
||||
"must_exist" : true,
|
||||
"create_parent" : true,
|
||||
"required" : false,
|
||||
"direction" : "output",
|
||||
"multiple" : false,
|
||||
"multiple_sep" : ";"
|
||||
},
|
||||
{
|
||||
"type" : "file",
|
||||
"name" : "--html",
|
||||
"description" : "Create the HTML report of the results. \n'*' wild card must be provided in the output file name. \nWild card will be replaced by the input file basename.\ne.g. \n --input \\"sample_1.fq\\"\n --html \\"*.html\\"\n would create an output html file named sample_1.html\n",
|
||||
"example" : [
|
||||
"*.html"
|
||||
],
|
||||
"must_exist" : true,
|
||||
"create_parent" : true,
|
||||
"required" : false,
|
||||
"direction" : "output",
|
||||
"multiple" : true,
|
||||
"multiple_sep" : ";"
|
||||
},
|
||||
{
|
||||
"type" : "file",
|
||||
"name" : "--zip",
|
||||
"description" : "Create the zip file(s) containing: html report, data, images, icons, summary, etc.\n'*' wild card must be provided in the output file name.\nWild card will be replaced by the input basename.\ne.g. \n --input \\"sample_1.fq\\"\n --html \\"*.zip\\"\n would create an output zip file named sample_1.zip\n",
|
||||
"example" : [
|
||||
"*.zip"
|
||||
],
|
||||
"must_exist" : true,
|
||||
"create_parent" : true,
|
||||
"required" : false,
|
||||
"direction" : "output",
|
||||
"multiple" : true,
|
||||
"multiple_sep" : ";"
|
||||
},
|
||||
{
|
||||
"type" : "file",
|
||||
"name" : "--summary",
|
||||
"description" : "Create the summary file(s).\n'*' wild card must be provided in the output file name.\nWild card will be replaced by the input basename.\ne.g. \n --input \\"sample_1.fq\\"\n --summary \\"*_summary.txt\\"\n would create an output summary.txt file named sample_1_summary.txt\n",
|
||||
"example" : [
|
||||
"*_summary.txt"
|
||||
],
|
||||
"must_exist" : true,
|
||||
"create_parent" : true,
|
||||
"required" : false,
|
||||
"direction" : "output",
|
||||
"multiple" : true,
|
||||
"multiple_sep" : ";"
|
||||
},
|
||||
{
|
||||
"type" : "file",
|
||||
"name" : "--data",
|
||||
"description" : "Create the data file(s).\n'*' wild card must be provided in the output file name.\nWild card will be replaced by the input basename.\ne.g. \n --input \\"sample_1.fq\\"\n --summary \\"*_data.txt\\"\n would create an output data.txt file named sample_1_data.txt\n",
|
||||
"example" : [
|
||||
"*_data.txt"
|
||||
],
|
||||
"must_exist" : true,
|
||||
"create_parent" : true,
|
||||
"required" : false,
|
||||
"direction" : "output",
|
||||
"multiple" : true,
|
||||
"multiple_sep" : ";"
|
||||
}
|
||||
]
|
||||
},
|
||||
{
|
||||
"name" : "Options",
|
||||
"arguments" : [
|
||||
{
|
||||
"type" : "boolean_true",
|
||||
"name" : "--casava",
|
||||
"description" : "Files come from raw casava output. Files in the same sample\ngroup (differing only by the group number) will be analysed\nas a set rather than individually. Sequences with the filter\nflag set in the header will be excluded from the analysis.\nFiles must have the same names given to them by casava\n(including being gzipped and ending with .gz) otherwise they\nwon't be grouped together correctly.\n",
|
||||
"direction" : "input"
|
||||
},
|
||||
{
|
||||
"type" : "boolean_true",
|
||||
"name" : "--nano",
|
||||
"description" : "Files come from nanopore sequences and are in fast5 format. In\nthis mode you can pass in directories to process and the program\nwill take in all fast5 files within those directories and produce\na single output file from the sequences found in all files.\n",
|
||||
"direction" : "input"
|
||||
},
|
||||
{
|
||||
"type" : "boolean_true",
|
||||
"name" : "--nofilter",
|
||||
"description" : "If running with --casava then don't remove read flagged by\ncasava as poor quality when performing the QC analysis.\n",
|
||||
"direction" : "input"
|
||||
},
|
||||
{
|
||||
"type" : "boolean_true",
|
||||
"name" : "--nogroup",
|
||||
"description" : "Disable grouping of bases for reads >50bp. \nAll reports will show data for every base in the read. \nWARNING: Using this option will cause fastqc to crash \nand burn if you use it on really long reads, and your \nplots may end up a ridiculous size. You have been warned!\n",
|
||||
"description" : "Disable grouping of bases for reads >50bp. \nAll reports will show data for every base in \nthe read. WARNING: When using this option, \nyour plots may end up a ridiculous size. You \nhave been warned!\n",
|
||||
"direction" : "input"
|
||||
},
|
||||
{
|
||||
"type" : "integer",
|
||||
"name" : "--min_length",
|
||||
"description" : "Sets an artificial lower limit on the length of the \nsequence to be shown in the report. As long as you \nset this to a value greater or equal to your longest \nread length then this will be the sequence length used \nto create your read groups. This can be useful for making\ndirectly comparable statistics from datasets with somewhat \nvariable read lengths.\n",
|
||||
"example" : [
|
||||
0
|
||||
],
|
||||
"required" : false,
|
||||
"direction" : "input",
|
||||
"multiple" : false,
|
||||
"multiple_sep" : ";"
|
||||
},
|
||||
{
|
||||
"type" : "string",
|
||||
"name" : "--format",
|
||||
"alternatives" : [
|
||||
"-f"
|
||||
],
|
||||
"description" : "Bypasses the normal sequence file format detection and \nforces the program to use the specified format. \nValid formats are bam, sam, bam_mapped, sam_mapped, and fastq.\n",
|
||||
"example" : [
|
||||
"bam"
|
||||
],
|
||||
"required" : false,
|
||||
"direction" : "input",
|
||||
"multiple" : false,
|
||||
"multiple_sep" : ";"
|
||||
},
|
||||
{
|
||||
"type" : "file",
|
||||
"name" : "--contaminants",
|
||||
"alternatives" : [
|
||||
"-c"
|
||||
],
|
||||
"description" : "Specifies a non-default file which contains the list \nof contaminants to screen overrepresented sequences against. \nThe file must contain sets of named contaminants in the form\nname[tab]sequence. Lines prefixed with a hash will be ignored.\n",
|
||||
"example" : [
|
||||
"contaminants.txt"
|
||||
],
|
||||
"name" : "--contaminents",
|
||||
"description" : "Specifies a non-default file which contains \nthe list of contaminants to screen \noverrepresented sequences against. The file \nmust contain sets of named contaminants in \nthe form name[tab]sequence. Lines prefixed \nwith a hash will be ignored. Default: \nhttps://github.com/smithlabcode/falco/blob/v1.2.5/Configuration/contaminant_list.txt\n",
|
||||
"must_exist" : true,
|
||||
"create_parent" : true,
|
||||
"required" : false,
|
||||
@@ -3221,13 +3100,7 @@ meta = [
|
||||
{
|
||||
"type" : "file",
|
||||
"name" : "--adapters",
|
||||
"alternatives" : [
|
||||
"-a"
|
||||
],
|
||||
"description" : "Specifies a non-default file which contains the list of \nadapter sequences which will be explicitly searched against \nthe library. The file must contain sets of named adapters \nin the form name[tab]sequence. Lines prefixed with a hash will be ignored.\n",
|
||||
"example" : [
|
||||
"adapters.txt"
|
||||
],
|
||||
"description" : "Specifies a non-default file which contains \nthe list of adapter sequences which will be \nexplicity searched against the library. The \nfile must contain sets of named adapters in \nthe form name[tab]sequence. Lines prefixed \nwith a hash will be ignored. Default:\nhttps://github.com/smithlabcode/falco/blob/v1.2.5/Configuration/adapter_list.txt\n",
|
||||
"must_exist" : true,
|
||||
"create_parent" : true,
|
||||
"required" : false,
|
||||
@@ -3238,13 +3111,7 @@ meta = [
|
||||
{
|
||||
"type" : "file",
|
||||
"name" : "--limits",
|
||||
"alternatives" : [
|
||||
"-l"
|
||||
],
|
||||
"description" : "Specifies a non-default file which contains \na set of criteria which will be used to determine \nthe warn/error limits for the various modules. \nThis file can also be used to selectively remove \nsome modules from the output altogether. The format \nneeds to mirror the default limits.txt file found in \nthe Configuration folder.\n",
|
||||
"example" : [
|
||||
"limits.txt"
|
||||
],
|
||||
"description" : "Specifies a non-default file which contains \na set of criteria which will be used to \ndetermine the warn/error limits for the \nvarious modules. This file can also be used \nto selectively remove some modules from the \noutput all together. The format needs to \nmirror the default limits.txt file found in \nthe Configuration folder. Default: \nhttps://github.com/smithlabcode/falco/blob/v1.2.5/Configuration/limits.txt\n",
|
||||
"must_exist" : true,
|
||||
"create_parent" : true,
|
||||
"required" : false,
|
||||
@@ -3254,13 +3121,13 @@ meta = [
|
||||
},
|
||||
{
|
||||
"type" : "integer",
|
||||
"name" : "--kmers",
|
||||
"name" : "--subsample",
|
||||
"alternatives" : [
|
||||
"-k"
|
||||
"-s"
|
||||
],
|
||||
"description" : "Specifies the length of Kmer to look for in the Kmer \ncontent module. Specified Kmer length must be between \n2 and 10. Default length is 7 if not specified.\n",
|
||||
"description" : "[Falco only] makes falco faster (but \npossibly less accurate) by only processing \nreads that are a multiple of this value (using \n0-based indexing to number reads).\n",
|
||||
"example" : [
|
||||
7
|
||||
10
|
||||
],
|
||||
"required" : false,
|
||||
"direction" : "input",
|
||||
@@ -3269,12 +3136,113 @@ meta = [
|
||||
},
|
||||
{
|
||||
"type" : "boolean_true",
|
||||
"name" : "--quiet",
|
||||
"name" : "--bisulfite",
|
||||
"alternatives" : [
|
||||
"-q"
|
||||
"-b"
|
||||
],
|
||||
"description" : "Suppress all progress messages on stdout and only report errors.\n",
|
||||
"description" : "[Falco only] reads are whole genome \nbisulfite sequencing, and more Ts and fewer \nCs are therefore expected and will be \naccounted for in base content.\n",
|
||||
"direction" : "input"
|
||||
},
|
||||
{
|
||||
"type" : "boolean_true",
|
||||
"name" : "--reverse_complement",
|
||||
"alternatives" : [
|
||||
"-r"
|
||||
],
|
||||
"description" : "[Falco only] The input is a \nreverse-complement. All modules will be \ntested by swapping A/T and C/G\n",
|
||||
"direction" : "input"
|
||||
},
|
||||
{
|
||||
"type" : "boolean_true",
|
||||
"name" : "--allow_empty_input",
|
||||
"description" : "Allow empty input files and generate empty output files without an error state.\n",
|
||||
"direction" : "input"
|
||||
}
|
||||
]
|
||||
},
|
||||
{
|
||||
"name" : "Output arguments",
|
||||
"arguments" : [
|
||||
{
|
||||
"type" : "file",
|
||||
"name" : "--outdir",
|
||||
"alternatives" : [
|
||||
"-o"
|
||||
],
|
||||
"description" : "Create all output files in the specified \noutput directory. FALCO-SPECIFIC: If the \ndirectory does not exists, the program will \ncreate it.\n",
|
||||
"example" : [
|
||||
"output"
|
||||
],
|
||||
"must_exist" : true,
|
||||
"create_parent" : true,
|
||||
"required" : true,
|
||||
"direction" : "output",
|
||||
"multiple" : false,
|
||||
"multiple_sep" : ";"
|
||||
},
|
||||
{
|
||||
"type" : "string",
|
||||
"name" : "--format",
|
||||
"alternatives" : [
|
||||
"-f"
|
||||
],
|
||||
"description" : "Bypasses the normal sequence file format \ndetection and forces the program to use the \nspecified format. Validformats are bam, sam, \nbam_mapped, sam_mapped, fastq, fq, fastq.gz \nor fq.gz.\n",
|
||||
"required" : false,
|
||||
"choices" : [
|
||||
"bam",
|
||||
"sam",
|
||||
"bam_mapped",
|
||||
"sam_mapped",
|
||||
"fastq",
|
||||
"fq",
|
||||
"fastq.gz",
|
||||
"fq.gz"
|
||||
],
|
||||
"direction" : "input",
|
||||
"multiple" : false,
|
||||
"multiple_sep" : ";"
|
||||
},
|
||||
{
|
||||
"type" : "file",
|
||||
"name" : "--data_filename",
|
||||
"alternatives" : [
|
||||
"-D"
|
||||
],
|
||||
"description" : "[Falco only] Specify filename for FastQC \ndata output (TXT). If not specified, it will \nbe called fastq_data.txt in either the input \nfile's directory or the one specified in the \n--output flag. Only available when running \nfalco with a single input.\n",
|
||||
"must_exist" : true,
|
||||
"create_parent" : true,
|
||||
"required" : false,
|
||||
"direction" : "output",
|
||||
"multiple" : false,
|
||||
"multiple_sep" : ";"
|
||||
},
|
||||
{
|
||||
"type" : "file",
|
||||
"name" : "--report_filename",
|
||||
"alternatives" : [
|
||||
"-R"
|
||||
],
|
||||
"description" : "[Falco only] Specify filename for FastQC \nreport output (HTML). If not specified, it \nwill be called fastq_report.html in either \nthe input file's directory or the one \nspecified in the --output flag. Only \navailable when running falco with a single \ninput.\n",
|
||||
"must_exist" : true,
|
||||
"create_parent" : true,
|
||||
"required" : false,
|
||||
"direction" : "output",
|
||||
"multiple" : false,
|
||||
"multiple_sep" : ";"
|
||||
},
|
||||
{
|
||||
"type" : "file",
|
||||
"name" : "--summary_filename",
|
||||
"alternatives" : [
|
||||
"-S"
|
||||
],
|
||||
"description" : "[Falco only] Specify filename for the short \nsummary output (TXT). If not specified, it \nwill be called fastq_report.html in either \nthe input file's directory or the one \nspecified in the --output flag. Only \navailable when running falco with a single \ninput.\n",
|
||||
"must_exist" : true,
|
||||
"create_parent" : true,
|
||||
"required" : false,
|
||||
"direction" : "output",
|
||||
"multiple" : false,
|
||||
"multiple_sep" : ";"
|
||||
}
|
||||
]
|
||||
}
|
||||
@@ -3286,12 +3254,16 @@ meta = [
|
||||
"is_executable" : true
|
||||
}
|
||||
],
|
||||
"description" : "FastQC - A high throughput sequence QC analysis tool.",
|
||||
"description" : "A C++ drop-in replacement of FastQC to assess the quality of sequence read data",
|
||||
"test_resources" : [
|
||||
{
|
||||
"type" : "bash_script",
|
||||
"path" : "test.sh",
|
||||
"is_executable" : true
|
||||
},
|
||||
{
|
||||
"type" : "file",
|
||||
"path" : "/src/_utils/test_helpers.sh"
|
||||
}
|
||||
],
|
||||
"status" : "enabled",
|
||||
@@ -3301,21 +3273,24 @@ meta = [
|
||||
},
|
||||
"requirements" : {
|
||||
"commands" : [
|
||||
"falco",
|
||||
"ps"
|
||||
]
|
||||
},
|
||||
"keywords" : [
|
||||
"Quality control",
|
||||
"BAM",
|
||||
"SAM",
|
||||
"FASTQ"
|
||||
"qc",
|
||||
"fastqc",
|
||||
"sequencing"
|
||||
],
|
||||
"license" : "GPL-3.0, Apache-2.0",
|
||||
"license" : "GPL-3.0",
|
||||
"references" : {
|
||||
"doi" : [
|
||||
"10.12688/f1000research.21142.2"
|
||||
]
|
||||
},
|
||||
"links" : {
|
||||
"repository" : "https://github.com/s-andrews/FastQC",
|
||||
"homepage" : "https://www.bioinformatics.babraham.ac.uk/projects/fastqc/",
|
||||
"documentation" : "https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/",
|
||||
"issue_tracker" : "https://github.com/s-andrews/FastQC/issues"
|
||||
"repository" : "https://github.com/smithlabcode/falco",
|
||||
"documentation" : "https://falco.readthedocs.io/en/latest/"
|
||||
},
|
||||
"runners" : [
|
||||
{
|
||||
@@ -3395,7 +3370,7 @@ meta = [
|
||||
{
|
||||
"type" : "docker",
|
||||
"id" : "docker",
|
||||
"image" : "biocontainers/fastqc:v0.11.9_cv8",
|
||||
"image" : "quay.io/biocontainers/falco:1.2.5--h077b44d_0",
|
||||
"target_registry" : "images.viash-hub.com",
|
||||
"target_tag" : "v0.4.1",
|
||||
"namespace_separator" : "/",
|
||||
@@ -3403,7 +3378,7 @@ meta = [
|
||||
{
|
||||
"type" : "docker",
|
||||
"run" : [
|
||||
"echo \\"fastqc: $(fastqc --version | sed -n 's/^FastQC //p')\\" > /var/software_versions.txt\n"
|
||||
"echo \\"falco: \\\\\\"$(falco -v | sed -n 's/^falco //p')\\\\\\"\\" > /var/software_versions.txt\n"
|
||||
]
|
||||
}
|
||||
]
|
||||
@@ -3414,10 +3389,10 @@ meta = [
|
||||
}
|
||||
],
|
||||
"build_info" : {
|
||||
"config" : "/workdir/root/repo/src/fastqc/config.vsh.yaml",
|
||||
"config" : "/workdir/root/repo/src/falco/config.vsh.yaml",
|
||||
"runner" : "nextflow",
|
||||
"engine" : "docker|native",
|
||||
"output" : "target/nextflow/fastqc",
|
||||
"output" : "target/nextflow/falco",
|
||||
"viash_version" : "0.9.4",
|
||||
"git_commit" : "69186bfc6beed075e81e10f17d24c4c999e87484",
|
||||
"git_remote" : "https://github.com/viash-hub/biobox"
|
||||
@@ -3460,27 +3435,22 @@ def innerWorkflowFactory(args) {
|
||||
def rawScript = '''set -e
|
||||
tempscript=".viash_script.sh"
|
||||
cat > "$tempscript" << VIASHMAIN
|
||||
#!/bin/bash
|
||||
|
||||
## VIASH START
|
||||
# The following code has been auto-generated by Viash.
|
||||
$( if [ ! -z ${VIASH_PAR_INPUT+x} ]; then echo "${VIASH_PAR_INPUT}" | sed "s#'#'\\"'\\"'#g;s#.*#par_input='&'#" ; else echo "# par_input="; fi )
|
||||
$( if [ ! -z ${VIASH_PAR_OUTDIR+x} ]; then echo "${VIASH_PAR_OUTDIR}" | sed "s#'#'\\"'\\"'#g;s#.*#par_outdir='&'#" ; else echo "# par_outdir="; fi )
|
||||
$( if [ ! -z ${VIASH_PAR_HTML+x} ]; then echo "${VIASH_PAR_HTML}" | sed "s#'#'\\"'\\"'#g;s#.*#par_html='&'#" ; else echo "# par_html="; fi )
|
||||
$( if [ ! -z ${VIASH_PAR_ZIP+x} ]; then echo "${VIASH_PAR_ZIP}" | sed "s#'#'\\"'\\"'#g;s#.*#par_zip='&'#" ; else echo "# par_zip="; fi )
|
||||
$( if [ ! -z ${VIASH_PAR_SUMMARY+x} ]; then echo "${VIASH_PAR_SUMMARY}" | sed "s#'#'\\"'\\"'#g;s#.*#par_summary='&'#" ; else echo "# par_summary="; fi )
|
||||
$( if [ ! -z ${VIASH_PAR_DATA+x} ]; then echo "${VIASH_PAR_DATA}" | sed "s#'#'\\"'\\"'#g;s#.*#par_data='&'#" ; else echo "# par_data="; fi )
|
||||
$( if [ ! -z ${VIASH_PAR_CASAVA+x} ]; then echo "${VIASH_PAR_CASAVA}" | sed "s#'#'\\"'\\"'#g;s#.*#par_casava='&'#" ; else echo "# par_casava="; fi )
|
||||
$( if [ ! -z ${VIASH_PAR_NANO+x} ]; then echo "${VIASH_PAR_NANO}" | sed "s#'#'\\"'\\"'#g;s#.*#par_nano='&'#" ; else echo "# par_nano="; fi )
|
||||
$( if [ ! -z ${VIASH_PAR_NOFILTER+x} ]; then echo "${VIASH_PAR_NOFILTER}" | sed "s#'#'\\"'\\"'#g;s#.*#par_nofilter='&'#" ; else echo "# par_nofilter="; fi )
|
||||
$( if [ ! -z ${VIASH_PAR_NOGROUP+x} ]; then echo "${VIASH_PAR_NOGROUP}" | sed "s#'#'\\"'\\"'#g;s#.*#par_nogroup='&'#" ; else echo "# par_nogroup="; fi )
|
||||
$( if [ ! -z ${VIASH_PAR_MIN_LENGTH+x} ]; then echo "${VIASH_PAR_MIN_LENGTH}" | sed "s#'#'\\"'\\"'#g;s#.*#par_min_length='&'#" ; else echo "# par_min_length="; fi )
|
||||
$( if [ ! -z ${VIASH_PAR_FORMAT+x} ]; then echo "${VIASH_PAR_FORMAT}" | sed "s#'#'\\"'\\"'#g;s#.*#par_format='&'#" ; else echo "# par_format="; fi )
|
||||
$( if [ ! -z ${VIASH_PAR_CONTAMINANTS+x} ]; then echo "${VIASH_PAR_CONTAMINANTS}" | sed "s#'#'\\"'\\"'#g;s#.*#par_contaminants='&'#" ; else echo "# par_contaminants="; fi )
|
||||
$( if [ ! -z ${VIASH_PAR_CONTAMINENTS+x} ]; then echo "${VIASH_PAR_CONTAMINENTS}" | sed "s#'#'\\"'\\"'#g;s#.*#par_contaminents='&'#" ; else echo "# par_contaminents="; fi )
|
||||
$( if [ ! -z ${VIASH_PAR_ADAPTERS+x} ]; then echo "${VIASH_PAR_ADAPTERS}" | sed "s#'#'\\"'\\"'#g;s#.*#par_adapters='&'#" ; else echo "# par_adapters="; fi )
|
||||
$( if [ ! -z ${VIASH_PAR_LIMITS+x} ]; then echo "${VIASH_PAR_LIMITS}" | sed "s#'#'\\"'\\"'#g;s#.*#par_limits='&'#" ; else echo "# par_limits="; fi )
|
||||
$( if [ ! -z ${VIASH_PAR_KMERS+x} ]; then echo "${VIASH_PAR_KMERS}" | sed "s#'#'\\"'\\"'#g;s#.*#par_kmers='&'#" ; else echo "# par_kmers="; fi )
|
||||
$( if [ ! -z ${VIASH_PAR_QUIET+x} ]; then echo "${VIASH_PAR_QUIET}" | sed "s#'#'\\"'\\"'#g;s#.*#par_quiet='&'#" ; else echo "# par_quiet="; fi )
|
||||
$( if [ ! -z ${VIASH_PAR_SUBSAMPLE+x} ]; then echo "${VIASH_PAR_SUBSAMPLE}" | sed "s#'#'\\"'\\"'#g;s#.*#par_subsample='&'#" ; else echo "# par_subsample="; fi )
|
||||
$( if [ ! -z ${VIASH_PAR_BISULFITE+x} ]; then echo "${VIASH_PAR_BISULFITE}" | sed "s#'#'\\"'\\"'#g;s#.*#par_bisulfite='&'#" ; else echo "# par_bisulfite="; fi )
|
||||
$( if [ ! -z ${VIASH_PAR_REVERSE_COMPLEMENT+x} ]; then echo "${VIASH_PAR_REVERSE_COMPLEMENT}" | sed "s#'#'\\"'\\"'#g;s#.*#par_reverse_complement='&'#" ; else echo "# par_reverse_complement="; fi )
|
||||
$( if [ ! -z ${VIASH_PAR_ALLOW_EMPTY_INPUT+x} ]; then echo "${VIASH_PAR_ALLOW_EMPTY_INPUT}" | sed "s#'#'\\"'\\"'#g;s#.*#par_allow_empty_input='&'#" ; else echo "# par_allow_empty_input="; fi )
|
||||
$( if [ ! -z ${VIASH_PAR_OUTDIR+x} ]; then echo "${VIASH_PAR_OUTDIR}" | sed "s#'#'\\"'\\"'#g;s#.*#par_outdir='&'#" ; else echo "# par_outdir="; fi )
|
||||
$( if [ ! -z ${VIASH_PAR_FORMAT+x} ]; then echo "${VIASH_PAR_FORMAT}" | sed "s#'#'\\"'\\"'#g;s#.*#par_format='&'#" ; else echo "# par_format="; fi )
|
||||
$( if [ ! -z ${VIASH_PAR_DATA_FILENAME+x} ]; then echo "${VIASH_PAR_DATA_FILENAME}" | sed "s#'#'\\"'\\"'#g;s#.*#par_data_filename='&'#" ; else echo "# par_data_filename="; fi )
|
||||
$( if [ ! -z ${VIASH_PAR_REPORT_FILENAME+x} ]; then echo "${VIASH_PAR_REPORT_FILENAME}" | sed "s#'#'\\"'\\"'#g;s#.*#par_report_filename='&'#" ; else echo "# par_report_filename="; fi )
|
||||
$( if [ ! -z ${VIASH_PAR_SUMMARY_FILENAME+x} ]; then echo "${VIASH_PAR_SUMMARY_FILENAME}" | sed "s#'#'\\"'\\"'#g;s#.*#par_summary_filename='&'#" ; else echo "# par_summary_filename="; fi )
|
||||
$( if [ ! -z ${VIASH_META_NAME+x} ]; then echo "${VIASH_META_NAME}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_name='&'#" ; else echo "# meta_name="; fi )
|
||||
$( if [ ! -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then echo "${VIASH_META_FUNCTIONALITY_NAME}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_functionality_name='&'#" ; else echo "# meta_functionality_name="; fi )
|
||||
$( if [ ! -z ${VIASH_META_RESOURCES_DIR+x} ]; then echo "${VIASH_META_RESOURCES_DIR}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_resources_dir='&'#" ; else echo "# meta_resources_dir="; fi )
|
||||
@@ -3501,112 +3471,33 @@ $( if [ ! -z ${VIASH_META_MEMORY_TIB+x} ]; then echo "${VIASH_META_MEMORY_TIB}"
|
||||
$( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo "${VIASH_META_MEMORY_PIB}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_memory_pib='&'#" ; else echo "# meta_memory_pib="; fi )
|
||||
|
||||
## VIASH END
|
||||
#!/bin/bash
|
||||
|
||||
# exit on error
|
||||
set -eo pipefail
|
||||
|
||||
# Check if both outputs are empty, at least one must be passed.
|
||||
if [[ -z "\\$par_outdir" ]] && [[ -z "\\$par_html" ]] && [[ -z "\\$par_zip" ]] && [[ -z "\\$par_summary" ]] && [[ -z "\\$par_data" ]]; then
|
||||
echo "Error: At least one of the output arguments (--outdir, --html, --zip, --summary, and --data) must be passed."
|
||||
exit 1
|
||||
fi
|
||||
[[ "\\$par_nogroup" == "false" ]] && unset par_nogroup
|
||||
[[ "\\$par_bisulfite" == "false" ]] && unset par_bisulfite
|
||||
[[ "\\$par_reverse_complement" == "false" ]] && unset par_reverse_complement
|
||||
[[ "\\$par_allow_empty_input" == "false" ]] && unset par_allow_empty_input
|
||||
|
||||
# unset flags
|
||||
unset_if_false=(
|
||||
par_casava
|
||||
par_nano
|
||||
par_nofilter
|
||||
par_extract
|
||||
par_noextract
|
||||
par_nogroup
|
||||
par_quiet
|
||||
)
|
||||
|
||||
for par in \\${unset_if_false[@]}; do
|
||||
test_val="\\${!par}"
|
||||
[[ "\\$test_val" == "false" ]] && unset \\$par
|
||||
done
|
||||
|
||||
tmpdir=\\$(mktemp -d "\\${meta_temp_dir}/\\${meta_name}-XXXXXXXX")
|
||||
function clean_up {
|
||||
rm -rf "\\$tmpdir"
|
||||
}
|
||||
trap clean_up EXIT
|
||||
|
||||
# Set output directory
|
||||
if [[ -n "\\$par_outdir" ]]; then
|
||||
if [[ ! -d "\\$par_outdir" ]]; then
|
||||
mkdir -p "\\$par_outdir"
|
||||
fi
|
||||
output_dir="\\$par_outdir"
|
||||
else
|
||||
output_dir="\\$tmpdir"
|
||||
fi
|
||||
|
||||
# Create input array
|
||||
IFS=";" read -ra input <<< \\$par_input
|
||||
|
||||
# Run fastqc
|
||||
fastqc \\\\
|
||||
--extract \\\\
|
||||
\\${par_casava:+--casava} \\\\
|
||||
\\${par_nano:+--nano} \\\\
|
||||
\\${par_nofilter:+--nofilter} \\\\
|
||||
\\$(which falco) \\\\
|
||||
\\${par_nogroup:+--nogroup} \\\\
|
||||
\\${par_min_length:+--min_length "\\$par_min_length"} \\\\
|
||||
\\${par_format:+--format "\\$par_format"} \\\\
|
||||
\\${par_contaminants:+--contaminants "\\$par_contaminants"} \\\\
|
||||
\\${par_adapters:+--adapters "\\$par_adapters"} \\\\
|
||||
\\${par_limits:+--limits "\\$par_limits"} \\\\
|
||||
\\${par_kmers:+--kmers "\\$par_kmers"} \\\\
|
||||
\\${par_quiet:+--quiet} \\\\
|
||||
\\${meta_cpus:+--threads "\\$meta_cpus"} \\\\
|
||||
\\${meta_temp_dir:+--dir "\\$meta_temp_dir"} \\\\
|
||||
--outdir "\\${output_dir}" \\\\
|
||||
"\\${input[@]}"
|
||||
|
||||
|
||||
# Move output files
|
||||
for file in "\\${input[@]}"; do
|
||||
# Removes everything after the first dot of the basename
|
||||
sample_name=\\$(basename "\\${file}" | sed 's/\\\\..*\\$//')
|
||||
if [[ -n "\\$par_html" ]]; then
|
||||
input_html="\\${output_dir}/\\${sample_name}_fastqc.html"
|
||||
if [[ ! -f "\\$input_html" ]]; then
|
||||
echo "WARNING: HTML file '\\$input_html' does not exist"
|
||||
else
|
||||
html_file="\\${par_html//\\\\*/\\$sample_name}"
|
||||
cp "\\$input_html" "\\$html_file"
|
||||
fi
|
||||
fi
|
||||
if [[ -n "\\$par_zip" ]]; then
|
||||
input_zip="\\${output_dir}/\\${sample_name}_fastqc.zip"
|
||||
if [[ ! -f "\\$input_zip" ]]; then
|
||||
echo "WARNING: ZIP file '\\$input_zip' does not exist"
|
||||
else
|
||||
zip_file="\\${par_zip//\\\\*/\\$sample_name}"
|
||||
cp "\\$input_zip" "\\$zip_file"
|
||||
fi
|
||||
fi
|
||||
if [[ -n "\\$par_summary" ]]; then
|
||||
summary_file="\\${output_dir}/\\${sample_name}_fastqc/summary.txt"
|
||||
if [[ ! -f "\\$summary_file" ]]; then
|
||||
echo "WARNING: Summary file '\\$summary_file' does not exist"
|
||||
else
|
||||
new_summary="\\${par_summary//\\\\*/\\$sample_name}"
|
||||
cp "\\$summary_file" "\\$new_summary"
|
||||
fi
|
||||
fi
|
||||
if [[ -n "\\$par_data" ]]; then
|
||||
data_file="\\${output_dir}/\\${sample_name}_fastqc/fastqc_data.txt"
|
||||
if [[ ! -f "\\$data_file" ]]; then
|
||||
echo "WARNING: Data file '\\$data_file' does not exist"
|
||||
else
|
||||
new_data="\\${par_data//\\\\*/\\$sample_name}"
|
||||
cp "\\$data_file" "\\$new_data"
|
||||
fi
|
||||
fi
|
||||
done
|
||||
\\${par_subsample:+-subsample \\$par_subsample} \\\\
|
||||
\\${par_bisulfite:+-bisulfite} \\\\
|
||||
\\${par_allow_empty_input:+-allow-empty-input} \\\\
|
||||
\\${par_reverse_complement:+-reverse-complement} \\\\
|
||||
\\${par_outdir:+--outdir "\\$par_outdir"} \\\\
|
||||
\\${par_format:+--format "\\$par_format"} \\\\
|
||||
\\${par_data_filename:+-data-filename "\\$par_data_filename"} \\\\
|
||||
\\${par_report_filename:+-report-filename "\\$par_report_filename"} \\\\
|
||||
\\${par_summary_filename:+-summary-filename "\\$par_summary_filename"} \\\\
|
||||
\\${input[*]}
|
||||
VIASHMAIN
|
||||
bash "$tempscript"
|
||||
'''
|
||||
@@ -3988,7 +3879,7 @@ meta["defaults"] = [
|
||||
directives: readJsonBlob('''{
|
||||
"container" : {
|
||||
"registry" : "images.viash-hub.com",
|
||||
"image" : "vsh/biobox/fastqc",
|
||||
"image" : "vsh/biobox/falco",
|
||||
"tag" : "v0.4.1"
|
||||
},
|
||||
"tag" : "$id"
|
||||
@@ -1,10 +1,10 @@
|
||||
manifest {
|
||||
name = 'fastqc'
|
||||
name = 'falco'
|
||||
mainScript = 'main.nf'
|
||||
nextflowVersion = '!>=20.12.1-edge'
|
||||
version = 'v0.4.1'
|
||||
description = 'FastQC - A high throughput sequence QC analysis tool.'
|
||||
author = 'Theodoro Gasperin Terra Camargo'
|
||||
description = 'A C++ drop-in replacement of FastQC to assess the quality of sequence read data'
|
||||
author = 'Toni Verbeiren'
|
||||
}
|
||||
|
||||
process.container = 'nextflow/bash:latest'
|
||||
@@ -0,0 +1,155 @@
|
||||
{
|
||||
"$schema": "https://json-schema.org/draft/2020-12/schema",
|
||||
"title": "falco",
|
||||
"description": "A C++ drop-in replacement of FastQC to assess the quality of sequence read data",
|
||||
"type": "object",
|
||||
"$defs": {
|
||||
"input arguments": {
|
||||
"title": "Input arguments",
|
||||
"type": "object",
|
||||
"description": "No description",
|
||||
"properties": {
|
||||
"input": {
|
||||
"type": "array",
|
||||
"items": {
|
||||
"type": "string"
|
||||
},
|
||||
"format": "path",
|
||||
"exists": true,
|
||||
"description": "input fastq files",
|
||||
"help_text": "Type: `file`, multiple: `True`, required, direction: `input`, example: `[\"input1.fastq;input2.fastq\"]`. "
|
||||
}
|
||||
}
|
||||
},
|
||||
"run arguments": {
|
||||
"title": "Run arguments",
|
||||
"type": "object",
|
||||
"description": "No description",
|
||||
"properties": {
|
||||
"nogroup": {
|
||||
"type": "boolean",
|
||||
"description": "Disable grouping of bases for reads >50bp",
|
||||
"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
|
||||
"default": false
|
||||
},
|
||||
"contaminents": {
|
||||
"type": "string",
|
||||
"format": "path",
|
||||
"description": "Specifies a non-default file which contains \nthe list of contaminants to screen \noverrepresented sequences against",
|
||||
"help_text": "Type: `file`, multiple: `False`, direction: `input`. "
|
||||
},
|
||||
"adapters": {
|
||||
"type": "string",
|
||||
"format": "path",
|
||||
"description": "Specifies a non-default file which contains \nthe list of adapter sequences which will be \nexplicity searched against the library",
|
||||
"help_text": "Type: `file`, multiple: `False`, direction: `input`. "
|
||||
},
|
||||
"limits": {
|
||||
"type": "string",
|
||||
"format": "path",
|
||||
"description": "Specifies a non-default file which contains \na set of criteria which will be used to \ndetermine the warn/error limits for the \nvarious modules",
|
||||
"help_text": "Type: `file`, multiple: `False`, direction: `input`. "
|
||||
},
|
||||
"subsample": {
|
||||
"type": "integer",
|
||||
"description": "[Falco only] makes falco faster (but \npossibly less accurate) by only processing \nreads that are a multiple of this value (using \n0-based indexing to number reads).\n",
|
||||
"help_text": "Type: `integer`, multiple: `False`, example: `10`. "
|
||||
},
|
||||
"bisulfite": {
|
||||
"type": "boolean",
|
||||
"description": "[Falco only] reads are whole genome \nbisulfite sequencing, and more Ts and fewer \nCs are therefore expected and will be \naccounted for in base content.\n",
|
||||
"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
|
||||
"default": false
|
||||
},
|
||||
"reverse_complement": {
|
||||
"type": "boolean",
|
||||
"description": "[Falco only] The input is a \nreverse-complement",
|
||||
"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
|
||||
"default": false
|
||||
},
|
||||
"allow_empty_input": {
|
||||
"type": "boolean",
|
||||
"description": "Allow empty input files and generate empty output files without an error state.\n",
|
||||
"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
|
||||
"default": false
|
||||
}
|
||||
}
|
||||
},
|
||||
"output arguments": {
|
||||
"title": "Output arguments",
|
||||
"type": "object",
|
||||
"description": "No description",
|
||||
"properties": {
|
||||
"outdir": {
|
||||
"type": "string",
|
||||
"format": "path",
|
||||
"description": "Create all output files in the specified \noutput directory",
|
||||
"help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.outdir\"`, direction: `output`, example: `\"output\"`. ",
|
||||
"default": "$id.$key.outdir"
|
||||
},
|
||||
"format": {
|
||||
"type": "string",
|
||||
"description": "Bypasses the normal sequence file format \ndetection and forces the program to use the \nspecified format",
|
||||
"help_text": "Type: `string`, multiple: `False`, choices: ``bam`, `sam`, `bam_mapped`, `sam_mapped`, `fastq`, `fq`, `fastq.gz`, `fq.gz``. ",
|
||||
"enum": [
|
||||
"bam",
|
||||
"sam",
|
||||
"bam_mapped",
|
||||
"sam_mapped",
|
||||
"fastq",
|
||||
"fq",
|
||||
"fastq.gz",
|
||||
"fq.gz"
|
||||
]
|
||||
},
|
||||
"data_filename": {
|
||||
"type": "string",
|
||||
"format": "path",
|
||||
"description": "[Falco only] Specify filename for FastQC \ndata output (TXT)",
|
||||
"help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.data_filename\"`, direction: `output`. ",
|
||||
"default": "$id.$key.data_filename"
|
||||
},
|
||||
"report_filename": {
|
||||
"type": "string",
|
||||
"format": "path",
|
||||
"description": "[Falco only] Specify filename for FastQC \nreport output (HTML)",
|
||||
"help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.report_filename\"`, direction: `output`. ",
|
||||
"default": "$id.$key.report_filename"
|
||||
},
|
||||
"summary_filename": {
|
||||
"type": "string",
|
||||
"format": "path",
|
||||
"description": "[Falco only] Specify filename for the short \nsummary output (TXT)",
|
||||
"help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.summary_filename\"`, direction: `output`. ",
|
||||
"default": "$id.$key.summary_filename"
|
||||
}
|
||||
}
|
||||
},
|
||||
"nextflow input-output arguments": {
|
||||
"title": "Nextflow input-output arguments",
|
||||
"type": "object",
|
||||
"description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.",
|
||||
"properties": {
|
||||
"publish_dir": {
|
||||
"type": "string",
|
||||
"description": "Path to an output directory.",
|
||||
"help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. "
|
||||
}
|
||||
}
|
||||
}
|
||||
},
|
||||
"allOf": [
|
||||
{
|
||||
"$ref": "#/$defs/input arguments"
|
||||
},
|
||||
{
|
||||
"$ref": "#/$defs/run arguments"
|
||||
},
|
||||
{
|
||||
"$ref": "#/$defs/output arguments"
|
||||
},
|
||||
{
|
||||
"$ref": "#/$defs/nextflow input-output arguments"
|
||||
}
|
||||
]
|
||||
}
|
||||
@@ -1,175 +0,0 @@
|
||||
{
|
||||
"$schema": "https://json-schema.org/draft/2020-12/schema",
|
||||
"title": "fastqc",
|
||||
"description": "FastQC - A high throughput sequence QC analysis tool.",
|
||||
"type": "object",
|
||||
"$defs": {
|
||||
"inputs": {
|
||||
"title": "Inputs",
|
||||
"type": "object",
|
||||
"description": "No description",
|
||||
"properties": {
|
||||
"input": {
|
||||
"type": "array",
|
||||
"items": {
|
||||
"type": "string"
|
||||
},
|
||||
"format": "path",
|
||||
"exists": true,
|
||||
"description": "FASTQ file(s) to be analyzed.\n",
|
||||
"help_text": "Type: `file`, multiple: `True`, required, direction: `input`, example: `[\"input.fq\"]`. "
|
||||
}
|
||||
}
|
||||
},
|
||||
"outputs": {
|
||||
"title": "Outputs",
|
||||
"type": "object",
|
||||
"description": "At least one of the output options (--html, --zip, --summary, --data) must be used.\n",
|
||||
"properties": {
|
||||
"outdir": {
|
||||
"type": "string",
|
||||
"format": "path",
|
||||
"description": "Output directory where the results will be saved.\n",
|
||||
"help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.outdir\"`, direction: `output`, example: `\"results\"`. ",
|
||||
"default": "$id.$key.outdir"
|
||||
},
|
||||
"html": {
|
||||
"type": "array",
|
||||
"items": {
|
||||
"type": "string"
|
||||
},
|
||||
"format": "path",
|
||||
"description": "Create the HTML report of the results",
|
||||
"help_text": "Type: `file`, multiple: `True`, default: `\"$id.$key.html_*.html\"`, direction: `output`, example: `[\"*.html\"]`. ",
|
||||
"default": "$id.$key.html_*.html"
|
||||
},
|
||||
"zip": {
|
||||
"type": "array",
|
||||
"items": {
|
||||
"type": "string"
|
||||
},
|
||||
"format": "path",
|
||||
"description": "Create the zip file(s) containing: html report, data, images, icons, summary, etc.\n'*' wild card must be provided in the output file name.\nWild card will be replaced by the input basename.\ne.g",
|
||||
"help_text": "Type: `file`, multiple: `True`, default: `\"$id.$key.zip_*.zip\"`, direction: `output`, example: `[\"*.zip\"]`. ",
|
||||
"default": "$id.$key.zip_*.zip"
|
||||
},
|
||||
"summary": {
|
||||
"type": "array",
|
||||
"items": {
|
||||
"type": "string"
|
||||
},
|
||||
"format": "path",
|
||||
"description": "Create the summary file(s).\n'*' wild card must be provided in the output file name.\nWild card will be replaced by the input basename.\ne.g",
|
||||
"help_text": "Type: `file`, multiple: `True`, default: `\"$id.$key.summary_*.txt\"`, direction: `output`, example: `[\"*_summary.txt\"]`. ",
|
||||
"default": "$id.$key.summary_*.txt"
|
||||
},
|
||||
"data": {
|
||||
"type": "array",
|
||||
"items": {
|
||||
"type": "string"
|
||||
},
|
||||
"format": "path",
|
||||
"description": "Create the data file(s).\n'*' wild card must be provided in the output file name.\nWild card will be replaced by the input basename.\ne.g",
|
||||
"help_text": "Type: `file`, multiple: `True`, default: `\"$id.$key.data_*.txt\"`, direction: `output`, example: `[\"*_data.txt\"]`. ",
|
||||
"default": "$id.$key.data_*.txt"
|
||||
}
|
||||
}
|
||||
},
|
||||
"options": {
|
||||
"title": "Options",
|
||||
"type": "object",
|
||||
"description": "No description",
|
||||
"properties": {
|
||||
"casava": {
|
||||
"type": "boolean",
|
||||
"description": "Files come from raw casava output",
|
||||
"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
|
||||
"default": false
|
||||
},
|
||||
"nano": {
|
||||
"type": "boolean",
|
||||
"description": "Files come from nanopore sequences and are in fast5 format",
|
||||
"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
|
||||
"default": false
|
||||
},
|
||||
"nofilter": {
|
||||
"type": "boolean",
|
||||
"description": "If running with --casava then don't remove read flagged by\ncasava as poor quality when performing the QC analysis.\n",
|
||||
"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
|
||||
"default": false
|
||||
},
|
||||
"nogroup": {
|
||||
"type": "boolean",
|
||||
"description": "Disable grouping of bases for reads >50bp",
|
||||
"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
|
||||
"default": false
|
||||
},
|
||||
"min_length": {
|
||||
"type": "integer",
|
||||
"description": "Sets an artificial lower limit on the length of the \nsequence to be shown in the report",
|
||||
"help_text": "Type: `integer`, multiple: `False`, example: `0`. "
|
||||
},
|
||||
"format": {
|
||||
"type": "string",
|
||||
"description": "Bypasses the normal sequence file format detection and \nforces the program to use the specified format",
|
||||
"help_text": "Type: `string`, multiple: `False`, example: `\"bam\"`. "
|
||||
},
|
||||
"contaminants": {
|
||||
"type": "string",
|
||||
"format": "path",
|
||||
"description": "Specifies a non-default file which contains the list \nof contaminants to screen overrepresented sequences against",
|
||||
"help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"contaminants.txt\"`. "
|
||||
},
|
||||
"adapters": {
|
||||
"type": "string",
|
||||
"format": "path",
|
||||
"description": "Specifies a non-default file which contains the list of \nadapter sequences which will be explicitly searched against \nthe library",
|
||||
"help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"adapters.txt\"`. "
|
||||
},
|
||||
"limits": {
|
||||
"type": "string",
|
||||
"format": "path",
|
||||
"description": "Specifies a non-default file which contains \na set of criteria which will be used to determine \nthe warn/error limits for the various modules",
|
||||
"help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"limits.txt\"`. "
|
||||
},
|
||||
"kmers": {
|
||||
"type": "integer",
|
||||
"description": "Specifies the length of Kmer to look for in the Kmer \ncontent module",
|
||||
"help_text": "Type: `integer`, multiple: `False`, example: `7`. "
|
||||
},
|
||||
"quiet": {
|
||||
"type": "boolean",
|
||||
"description": "Suppress all progress messages on stdout and only report errors.\n",
|
||||
"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
|
||||
"default": false
|
||||
}
|
||||
}
|
||||
},
|
||||
"nextflow input-output arguments": {
|
||||
"title": "Nextflow input-output arguments",
|
||||
"type": "object",
|
||||
"description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.",
|
||||
"properties": {
|
||||
"publish_dir": {
|
||||
"type": "string",
|
||||
"description": "Path to an output directory.",
|
||||
"help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. "
|
||||
}
|
||||
}
|
||||
}
|
||||
},
|
||||
"allOf": [
|
||||
{
|
||||
"$ref": "#/$defs/inputs"
|
||||
},
|
||||
{
|
||||
"$ref": "#/$defs/outputs"
|
||||
},
|
||||
{
|
||||
"$ref": "#/$defs/options"
|
||||
},
|
||||
{
|
||||
"$ref": "#/$defs/nextflow input-output arguments"
|
||||
}
|
||||
]
|
||||
}
|
||||
@@ -1,6 +1,6 @@
|
||||
name: "interop_summary_to_csv"
|
||||
namespace: "io"
|
||||
version: "v0.6.3"
|
||||
version: "v0.6.4"
|
||||
argument_groups:
|
||||
- name: "Input arguments"
|
||||
arguments:
|
||||
@@ -135,7 +135,7 @@ engines:
|
||||
id: "docker"
|
||||
image: "debian:stable-slim"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "v0.6.3"
|
||||
target_tag: "v0.6.4"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "apt"
|
||||
@@ -160,11 +160,11 @@ build_info:
|
||||
output: "target/executable/io/interop_summary_to_csv"
|
||||
executable: "target/executable/io/interop_summary_to_csv/interop_summary_to_csv"
|
||||
viash_version: "0.9.4"
|
||||
git_commit: "459033886f31de68cf97477867ff26e27ae6d98e"
|
||||
git_commit: "dc228b2b4eebe9fe93fec86af537cf8211c3abec"
|
||||
git_remote: "https://github.com/viash-hub/demultiplex"
|
||||
package_config:
|
||||
name: "demultiplex"
|
||||
version: "v0.6.3"
|
||||
version: "v0.6.4"
|
||||
description: "Demultiplexing pipeline\n"
|
||||
info:
|
||||
test_resources:
|
||||
@@ -180,7 +180,7 @@ package_config:
|
||||
)'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'v0.6.3'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'v0.6.4'"
|
||||
keywords:
|
||||
- "bioinformatics"
|
||||
- "sequence"
|
||||
|
||||
@@ -1,5 +1,5 @@
|
||||
name: demultiplex
|
||||
version: v0.6.3
|
||||
version: v0.6.4
|
||||
description: |
|
||||
Demultiplexing pipeline
|
||||
license: MIT
|
||||
|
||||
@@ -1,6 +1,6 @@
|
||||
#!/usr/bin/env bash
|
||||
|
||||
# interop_summary_to_csv v0.6.3
|
||||
# interop_summary_to_csv v0.6.4
|
||||
#
|
||||
# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
|
||||
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
|
||||
@@ -454,10 +454,10 @@ tar -C /tmp/ --no-same-owner --no-same-permissions -xvf /tmp/interop.tar.gz && \
|
||||
mv /tmp/interop-1.3.1-Linux-GNU/bin/index-summary /tmp/interop-1.3.1-Linux-GNU/bin/summary /usr/local/bin/
|
||||
|
||||
LABEL org.opencontainers.image.description="Companion container for running component io interop_summary_to_csv"
|
||||
LABEL org.opencontainers.image.created="2025-11-05T08:18:10Z"
|
||||
LABEL org.opencontainers.image.created="2025-11-19T07:56:11Z"
|
||||
LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
|
||||
LABEL org.opencontainers.image.revision="459033886f31de68cf97477867ff26e27ae6d98e"
|
||||
LABEL org.opencontainers.image.version="v0.6.3"
|
||||
LABEL org.opencontainers.image.revision="dc228b2b4eebe9fe93fec86af537cf8211c3abec"
|
||||
LABEL org.opencontainers.image.version="v0.6.4"
|
||||
|
||||
VIASHDOCKER
|
||||
fi
|
||||
@@ -574,7 +574,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
|
||||
|
||||
# ViashHelp: Display helpful explanation about this executable
|
||||
function ViashHelp {
|
||||
echo "interop_summary_to_csv v0.6.3"
|
||||
echo "interop_summary_to_csv v0.6.4"
|
||||
echo ""
|
||||
echo "Input arguments:"
|
||||
echo " --input"
|
||||
@@ -635,7 +635,7 @@ while [[ $# -gt 0 ]]; do
|
||||
shift 1
|
||||
;;
|
||||
--version)
|
||||
echo "interop_summary_to_csv v0.6.3"
|
||||
echo "interop_summary_to_csv v0.6.4"
|
||||
exit
|
||||
;;
|
||||
--input)
|
||||
@@ -759,7 +759,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
|
||||
|
||||
# determine docker image id
|
||||
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
|
||||
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/interop_summary_to_csv:v0.6.3'
|
||||
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/interop_summary_to_csv:v0.6.4'
|
||||
fi
|
||||
|
||||
# print dockerfile
|
||||
|
||||
@@ -1,6 +1,6 @@
|
||||
name: "publish"
|
||||
namespace: "io"
|
||||
version: "v0.6.3"
|
||||
version: "v0.6.4"
|
||||
argument_groups:
|
||||
- name: "Input arguments"
|
||||
arguments:
|
||||
@@ -204,7 +204,7 @@ engines:
|
||||
id: "docker"
|
||||
image: "debian:stable-slim"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "v0.6.3"
|
||||
target_tag: "v0.6.4"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "apt"
|
||||
@@ -222,11 +222,11 @@ build_info:
|
||||
output: "target/executable/io/publish"
|
||||
executable: "target/executable/io/publish/publish"
|
||||
viash_version: "0.9.4"
|
||||
git_commit: "459033886f31de68cf97477867ff26e27ae6d98e"
|
||||
git_commit: "dc228b2b4eebe9fe93fec86af537cf8211c3abec"
|
||||
git_remote: "https://github.com/viash-hub/demultiplex"
|
||||
package_config:
|
||||
name: "demultiplex"
|
||||
version: "v0.6.3"
|
||||
version: "v0.6.4"
|
||||
description: "Demultiplexing pipeline\n"
|
||||
info:
|
||||
test_resources:
|
||||
@@ -242,7 +242,7 @@ package_config:
|
||||
)'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'v0.6.3'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'v0.6.4'"
|
||||
keywords:
|
||||
- "bioinformatics"
|
||||
- "sequence"
|
||||
|
||||
@@ -1,5 +1,5 @@
|
||||
name: demultiplex
|
||||
version: v0.6.3
|
||||
version: v0.6.4
|
||||
description: |
|
||||
Demultiplexing pipeline
|
||||
license: MIT
|
||||
|
||||
@@ -1,6 +1,6 @@
|
||||
#!/usr/bin/env bash
|
||||
|
||||
# publish v0.6.3
|
||||
# publish v0.6.4
|
||||
#
|
||||
# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
|
||||
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
|
||||
@@ -450,10 +450,10 @@ RUN apt-get update && \
|
||||
rm -rf /var/lib/apt/lists/*
|
||||
|
||||
LABEL org.opencontainers.image.description="Companion container for running component io publish"
|
||||
LABEL org.opencontainers.image.created="2025-11-05T08:18:09Z"
|
||||
LABEL org.opencontainers.image.created="2025-11-19T07:56:10Z"
|
||||
LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
|
||||
LABEL org.opencontainers.image.revision="459033886f31de68cf97477867ff26e27ae6d98e"
|
||||
LABEL org.opencontainers.image.version="v0.6.3"
|
||||
LABEL org.opencontainers.image.revision="dc228b2b4eebe9fe93fec86af537cf8211c3abec"
|
||||
LABEL org.opencontainers.image.version="v0.6.4"
|
||||
|
||||
VIASHDOCKER
|
||||
fi
|
||||
@@ -570,7 +570,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
|
||||
|
||||
# ViashHelp: Display helpful explanation about this executable
|
||||
function ViashHelp {
|
||||
echo "publish v0.6.3"
|
||||
echo "publish v0.6.4"
|
||||
echo ""
|
||||
echo "Publish the processed results of the run"
|
||||
echo ""
|
||||
@@ -662,7 +662,7 @@ while [[ $# -gt 0 ]]; do
|
||||
shift 1
|
||||
;;
|
||||
--version)
|
||||
echo "publish v0.6.3"
|
||||
echo "publish v0.6.4"
|
||||
exit
|
||||
;;
|
||||
--input)
|
||||
@@ -869,7 +869,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
|
||||
|
||||
# determine docker image id
|
||||
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
|
||||
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/publish:v0.6.3'
|
||||
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/publish:v0.6.4'
|
||||
fi
|
||||
|
||||
# print dockerfile
|
||||
@@ -1320,7 +1320,7 @@ do
|
||||
mkdir -p \$(dirname "\$output_location") && echo "Containing directory \$output_location created"
|
||||
|
||||
echo "Copying files..."
|
||||
cp -rL "\$input_location" "\$output_location"
|
||||
cp -a --keep-directory-symlink "\$input_location" "\$output_location"
|
||||
|
||||
echo "Output files for \$output_location:"
|
||||
ls "\$output_location"
|
||||
@@ -1331,7 +1331,7 @@ mkdir -p "\$par_output_sample_qc"
|
||||
IFS=";" read -ra sample_qc_inputs <<< \$par_input_sample_qc
|
||||
for qc_dir in "\${sample_qc_inputs[@]}"; do
|
||||
echo "Copying contents of \$qc_dir"
|
||||
find -H -D exec "\$qc_dir" -type f -maxdepth 1 -exec cp -t "\$par_output_sample_qc" {} +
|
||||
find -H -D exec "\$qc_dir" -type f -maxdepth 1 -exec cp -a --keep-directory-symlink -t "\$par_output_sample_qc" {} +
|
||||
done
|
||||
VIASHMAIN
|
||||
bash "\$tempscript" &
|
||||
|
||||
@@ -1,6 +1,6 @@
|
||||
name: "untar"
|
||||
namespace: "io"
|
||||
version: "v0.6.3"
|
||||
version: "v0.6.4"
|
||||
argument_groups:
|
||||
- name: "Input arguments"
|
||||
arguments:
|
||||
@@ -141,7 +141,7 @@ engines:
|
||||
id: "docker"
|
||||
image: "debian:stable-slim"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "v0.6.3"
|
||||
target_tag: "v0.6.4"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "apt"
|
||||
@@ -159,11 +159,11 @@ build_info:
|
||||
output: "target/executable/io/untar"
|
||||
executable: "target/executable/io/untar/untar"
|
||||
viash_version: "0.9.4"
|
||||
git_commit: "459033886f31de68cf97477867ff26e27ae6d98e"
|
||||
git_commit: "dc228b2b4eebe9fe93fec86af537cf8211c3abec"
|
||||
git_remote: "https://github.com/viash-hub/demultiplex"
|
||||
package_config:
|
||||
name: "demultiplex"
|
||||
version: "v0.6.3"
|
||||
version: "v0.6.4"
|
||||
description: "Demultiplexing pipeline\n"
|
||||
info:
|
||||
test_resources:
|
||||
@@ -179,7 +179,7 @@ package_config:
|
||||
)'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'v0.6.3'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'v0.6.4'"
|
||||
keywords:
|
||||
- "bioinformatics"
|
||||
- "sequence"
|
||||
|
||||
@@ -1,5 +1,5 @@
|
||||
name: demultiplex
|
||||
version: v0.6.3
|
||||
version: v0.6.4
|
||||
description: |
|
||||
Demultiplexing pipeline
|
||||
license: MIT
|
||||
|
||||
@@ -1,6 +1,6 @@
|
||||
#!/usr/bin/env bash
|
||||
|
||||
# untar v0.6.3
|
||||
# untar v0.6.4
|
||||
#
|
||||
# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
|
||||
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
|
||||
@@ -450,10 +450,10 @@ RUN apt-get update && \
|
||||
rm -rf /var/lib/apt/lists/*
|
||||
|
||||
LABEL org.opencontainers.image.description="Companion container for running component io untar"
|
||||
LABEL org.opencontainers.image.created="2025-11-05T08:18:10Z"
|
||||
LABEL org.opencontainers.image.created="2025-11-19T07:56:11Z"
|
||||
LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
|
||||
LABEL org.opencontainers.image.revision="459033886f31de68cf97477867ff26e27ae6d98e"
|
||||
LABEL org.opencontainers.image.version="v0.6.3"
|
||||
LABEL org.opencontainers.image.revision="dc228b2b4eebe9fe93fec86af537cf8211c3abec"
|
||||
LABEL org.opencontainers.image.version="v0.6.4"
|
||||
|
||||
VIASHDOCKER
|
||||
fi
|
||||
@@ -570,7 +570,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
|
||||
|
||||
# ViashHelp: Display helpful explanation about this executable
|
||||
function ViashHelp {
|
||||
echo "untar v0.6.3"
|
||||
echo "untar v0.6.4"
|
||||
echo ""
|
||||
echo "Unpack a .tar file. When the contents of the .tar file is just a single"
|
||||
echo "directory,"
|
||||
@@ -641,7 +641,7 @@ while [[ $# -gt 0 ]]; do
|
||||
shift 1
|
||||
;;
|
||||
--version)
|
||||
echo "untar v0.6.3"
|
||||
echo "untar v0.6.4"
|
||||
exit
|
||||
;;
|
||||
--input)
|
||||
@@ -771,7 +771,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
|
||||
|
||||
# determine docker image id
|
||||
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
|
||||
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/untar:v0.6.3'
|
||||
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/untar:v0.6.4'
|
||||
fi
|
||||
|
||||
# print dockerfile
|
||||
|
||||
@@ -1,6 +1,6 @@
|
||||
name: "combine_samples"
|
||||
namespace: "dataflow"
|
||||
version: "v0.6.3"
|
||||
version: "v0.6.4"
|
||||
argument_groups:
|
||||
- name: "Input arguments"
|
||||
arguments:
|
||||
@@ -168,11 +168,11 @@ build_info:
|
||||
output: "target/nextflow/dataflow/combine_samples"
|
||||
executable: "target/nextflow/dataflow/combine_samples/main.nf"
|
||||
viash_version: "0.9.4"
|
||||
git_commit: "459033886f31de68cf97477867ff26e27ae6d98e"
|
||||
git_commit: "dc228b2b4eebe9fe93fec86af537cf8211c3abec"
|
||||
git_remote: "https://github.com/viash-hub/demultiplex"
|
||||
package_config:
|
||||
name: "demultiplex"
|
||||
version: "v0.6.3"
|
||||
version: "v0.6.4"
|
||||
description: "Demultiplexing pipeline\n"
|
||||
info:
|
||||
test_resources:
|
||||
@@ -188,7 +188,7 @@ package_config:
|
||||
)'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'v0.6.3'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'v0.6.4'"
|
||||
keywords:
|
||||
- "bioinformatics"
|
||||
- "sequence"
|
||||
|
||||
@@ -1,5 +1,5 @@
|
||||
name: demultiplex
|
||||
version: v0.6.3
|
||||
version: v0.6.4
|
||||
description: |
|
||||
Demultiplexing pipeline
|
||||
license: MIT
|
||||
|
||||
@@ -1,4 +1,4 @@
|
||||
// combine_samples v0.6.3
|
||||
// combine_samples v0.6.4
|
||||
//
|
||||
// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
|
||||
// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
|
||||
@@ -3032,7 +3032,7 @@ meta = [
|
||||
"config": processConfig(readJsonBlob('''{
|
||||
"name" : "combine_samples",
|
||||
"namespace" : "dataflow",
|
||||
"version" : "v0.6.3",
|
||||
"version" : "v0.6.4",
|
||||
"argument_groups" : [
|
||||
{
|
||||
"name" : "Input arguments",
|
||||
@@ -3235,12 +3235,12 @@ meta = [
|
||||
"engine" : "native|native",
|
||||
"output" : "target/nextflow/dataflow/combine_samples",
|
||||
"viash_version" : "0.9.4",
|
||||
"git_commit" : "459033886f31de68cf97477867ff26e27ae6d98e",
|
||||
"git_commit" : "dc228b2b4eebe9fe93fec86af537cf8211c3abec",
|
||||
"git_remote" : "https://github.com/viash-hub/demultiplex"
|
||||
},
|
||||
"package_config" : {
|
||||
"name" : "demultiplex",
|
||||
"version" : "v0.6.3",
|
||||
"version" : "v0.6.4",
|
||||
"description" : "Demultiplexing pipeline\n",
|
||||
"info" : {
|
||||
"test_resources" : [
|
||||
@@ -3257,7 +3257,7 @@ meta = [
|
||||
".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
|
||||
".engines += { type: \\"native\\" }",
|
||||
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
|
||||
".engines[.type == 'docker'].target_tag := 'v0.6.3'"
|
||||
".engines[.type == 'docker'].target_tag := 'v0.6.4'"
|
||||
],
|
||||
"keywords" : [
|
||||
"bioinformatics",
|
||||
|
||||
@@ -2,7 +2,7 @@ manifest {
|
||||
name = 'dataflow/combine_samples'
|
||||
mainScript = 'main.nf'
|
||||
nextflowVersion = '!>=20.12.1-edge'
|
||||
version = 'v0.6.3'
|
||||
version = 'v0.6.4'
|
||||
description = 'Combine fastq files from across samples into one event with a list of fastq files per orientation.'
|
||||
}
|
||||
|
||||
|
||||
@@ -1,6 +1,6 @@
|
||||
name: "gather_fastqs_and_validate"
|
||||
namespace: "dataflow"
|
||||
version: "v0.6.3"
|
||||
version: "v0.6.4"
|
||||
argument_groups:
|
||||
- name: "Input arguments"
|
||||
arguments:
|
||||
@@ -159,11 +159,11 @@ build_info:
|
||||
output: "target/nextflow/dataflow/gather_fastqs_and_validate"
|
||||
executable: "target/nextflow/dataflow/gather_fastqs_and_validate/main.nf"
|
||||
viash_version: "0.9.4"
|
||||
git_commit: "459033886f31de68cf97477867ff26e27ae6d98e"
|
||||
git_commit: "dc228b2b4eebe9fe93fec86af537cf8211c3abec"
|
||||
git_remote: "https://github.com/viash-hub/demultiplex"
|
||||
package_config:
|
||||
name: "demultiplex"
|
||||
version: "v0.6.3"
|
||||
version: "v0.6.4"
|
||||
description: "Demultiplexing pipeline\n"
|
||||
info:
|
||||
test_resources:
|
||||
@@ -179,7 +179,7 @@ package_config:
|
||||
)'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'v0.6.3'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'v0.6.4'"
|
||||
keywords:
|
||||
- "bioinformatics"
|
||||
- "sequence"
|
||||
|
||||
@@ -1,5 +1,5 @@
|
||||
name: demultiplex
|
||||
version: v0.6.3
|
||||
version: v0.6.4
|
||||
description: |
|
||||
Demultiplexing pipeline
|
||||
license: MIT
|
||||
|
||||
@@ -1,4 +1,4 @@
|
||||
// gather_fastqs_and_validate v0.6.3
|
||||
// gather_fastqs_and_validate v0.6.4
|
||||
//
|
||||
// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
|
||||
// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
|
||||
@@ -3032,7 +3032,7 @@ meta = [
|
||||
"config": processConfig(readJsonBlob('''{
|
||||
"name" : "gather_fastqs_and_validate",
|
||||
"namespace" : "dataflow",
|
||||
"version" : "v0.6.3",
|
||||
"version" : "v0.6.4",
|
||||
"argument_groups" : [
|
||||
{
|
||||
"name" : "Input arguments",
|
||||
@@ -3232,12 +3232,12 @@ meta = [
|
||||
"engine" : "native|native",
|
||||
"output" : "target/nextflow/dataflow/gather_fastqs_and_validate",
|
||||
"viash_version" : "0.9.4",
|
||||
"git_commit" : "459033886f31de68cf97477867ff26e27ae6d98e",
|
||||
"git_commit" : "dc228b2b4eebe9fe93fec86af537cf8211c3abec",
|
||||
"git_remote" : "https://github.com/viash-hub/demultiplex"
|
||||
},
|
||||
"package_config" : {
|
||||
"name" : "demultiplex",
|
||||
"version" : "v0.6.3",
|
||||
"version" : "v0.6.4",
|
||||
"description" : "Demultiplexing pipeline\n",
|
||||
"info" : {
|
||||
"test_resources" : [
|
||||
@@ -3254,7 +3254,7 @@ meta = [
|
||||
".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
|
||||
".engines += { type: \\"native\\" }",
|
||||
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
|
||||
".engines[.type == 'docker'].target_tag := 'v0.6.3'"
|
||||
".engines[.type == 'docker'].target_tag := 'v0.6.4'"
|
||||
],
|
||||
"keywords" : [
|
||||
"bioinformatics",
|
||||
|
||||
@@ -2,7 +2,7 @@ manifest {
|
||||
name = 'dataflow/gather_fastqs_and_validate'
|
||||
mainScript = 'main.nf'
|
||||
nextflowVersion = '!>=20.12.1-edge'
|
||||
version = 'v0.6.3'
|
||||
version = 'v0.6.4'
|
||||
description = 'From a directory containing fastq files, gather the files per sample \nand validate according to the contents of the sample sheet.\n'
|
||||
}
|
||||
|
||||
|
||||
@@ -1,5 +1,5 @@
|
||||
name: "demultiplex"
|
||||
version: "v0.6.3"
|
||||
version: "v0.6.4"
|
||||
argument_groups:
|
||||
- name: "Input arguments"
|
||||
arguments:
|
||||
@@ -171,7 +171,7 @@ dependencies:
|
||||
type: "vsh"
|
||||
repo: "biobox"
|
||||
tag: "v0.4.1"
|
||||
- name: "fastqc"
|
||||
- name: "falco"
|
||||
repository:
|
||||
type: "vsh"
|
||||
repo: "biobox"
|
||||
@@ -268,7 +268,7 @@ build_info:
|
||||
output: "target/nextflow/demultiplex"
|
||||
executable: "target/nextflow/demultiplex/main.nf"
|
||||
viash_version: "0.9.4"
|
||||
git_commit: "459033886f31de68cf97477867ff26e27ae6d98e"
|
||||
git_commit: "dc228b2b4eebe9fe93fec86af537cf8211c3abec"
|
||||
git_remote: "https://github.com/viash-hub/demultiplex"
|
||||
dependencies:
|
||||
- "target/nextflow/io/untar"
|
||||
@@ -277,12 +277,12 @@ build_info:
|
||||
- "target/nextflow/dataflow/combine_samples"
|
||||
- "target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/bcl_convert"
|
||||
- "target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/bases2fastq"
|
||||
- "target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/fastqc"
|
||||
- "target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/falco"
|
||||
- "target/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/multiqc"
|
||||
- "target/nextflow/detect_demultiplexer"
|
||||
package_config:
|
||||
name: "demultiplex"
|
||||
version: "v0.6.3"
|
||||
version: "v0.6.4"
|
||||
description: "Demultiplexing pipeline\n"
|
||||
info:
|
||||
test_resources:
|
||||
@@ -298,7 +298,7 @@ package_config:
|
||||
)'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'v0.6.3'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'v0.6.4'"
|
||||
keywords:
|
||||
- "bioinformatics"
|
||||
- "sequence"
|
||||
|
||||
@@ -1,5 +1,5 @@
|
||||
name: demultiplex
|
||||
version: v0.6.3
|
||||
version: v0.6.4
|
||||
description: |
|
||||
Demultiplexing pipeline
|
||||
license: MIT
|
||||
|
||||
@@ -1,4 +1,4 @@
|
||||
// demultiplex v0.6.3
|
||||
// demultiplex v0.6.4
|
||||
//
|
||||
// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
|
||||
// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
|
||||
@@ -3031,7 +3031,7 @@ meta = [
|
||||
"resources_dir": moduleDir.toRealPath().normalize(),
|
||||
"config": processConfig(readJsonBlob('''{
|
||||
"name" : "demultiplex",
|
||||
"version" : "v0.6.3",
|
||||
"version" : "v0.6.4",
|
||||
"argument_groups" : [
|
||||
{
|
||||
"name" : "Input arguments",
|
||||
@@ -3258,7 +3258,7 @@ meta = [
|
||||
}
|
||||
},
|
||||
{
|
||||
"name" : "fastqc",
|
||||
"name" : "falco",
|
||||
"repository" : {
|
||||
"type" : "vsh",
|
||||
"repo" : "biobox",
|
||||
@@ -3380,12 +3380,12 @@ meta = [
|
||||
"engine" : "native|native",
|
||||
"output" : "target/nextflow/demultiplex",
|
||||
"viash_version" : "0.9.4",
|
||||
"git_commit" : "459033886f31de68cf97477867ff26e27ae6d98e",
|
||||
"git_commit" : "dc228b2b4eebe9fe93fec86af537cf8211c3abec",
|
||||
"git_remote" : "https://github.com/viash-hub/demultiplex"
|
||||
},
|
||||
"package_config" : {
|
||||
"name" : "demultiplex",
|
||||
"version" : "v0.6.3",
|
||||
"version" : "v0.6.4",
|
||||
"description" : "Demultiplexing pipeline\n",
|
||||
"info" : {
|
||||
"test_resources" : [
|
||||
@@ -3402,7 +3402,7 @@ meta = [
|
||||
".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
|
||||
".engines += { type: \\"native\\" }",
|
||||
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
|
||||
".engines[.type == 'docker'].target_tag := 'v0.6.3'"
|
||||
".engines[.type == 'docker'].target_tag := 'v0.6.4'"
|
||||
],
|
||||
"keywords" : [
|
||||
"bioinformatics",
|
||||
@@ -3428,7 +3428,7 @@ include { interop_summary_to_csv } from "${meta.resources_dir}/../../nextflow/io
|
||||
include { combine_samples } from "${meta.resources_dir}/../../nextflow/dataflow/combine_samples/main.nf"
|
||||
include { bcl_convert } from "${meta.root_dir}/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/bcl_convert/main.nf"
|
||||
include { bases2fastq } from "${meta.root_dir}/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/bases2fastq/main.nf"
|
||||
include { fastqc } from "${meta.root_dir}/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/fastqc/main.nf"
|
||||
include { falco } from "${meta.root_dir}/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/falco/main.nf"
|
||||
include { multiqc } from "${meta.root_dir}/dependencies/vsh/vsh/biobox/v0.4.1/nextflow/multiqc/main.nf"
|
||||
include { detect_demultiplexer } from "${meta.resources_dir}/../../nextflow/detect_demultiplexer/main.nf"
|
||||
|
||||
@@ -3549,25 +3549,35 @@ workflow run_wf {
|
||||
],
|
||||
)
|
||||
|
||||
output_ch = samples_ch
|
||||
| fastqc.run(
|
||||
output_ch = samples_ch
|
||||
| falco.run(
|
||||
directives: [label: ["lowcpu", "midmem"]],
|
||||
fromState: {id, state ->
|
||||
def output_base = "$id/qc/fastqc/*"
|
||||
[
|
||||
"input": [state.fastq_forward, state.fastq_reverse],
|
||||
"html": "${output_base}_fastqc_report.html",
|
||||
"summary": "${output_base}_summary.txt",
|
||||
"data": "${output_base}_fastqc_data.txt",
|
||||
def input = state.fastq_forward + state.fastq_reverse
|
||||
def state_mapping = [
|
||||
"input": input,
|
||||
"outdir": "$id/qc/falco",
|
||||
"summary_filename": null,
|
||||
"report_filename": null,
|
||||
"data_filename": null,
|
||||
"allow_empty_input": true
|
||||
]
|
||||
// When a single FASTQ is being processed, Falco does not automatically
|
||||
// determine the basename from the input file. But this can be done manually here.
|
||||
if (input.size() == 1) {
|
||||
def basename = input[0].name
|
||||
state_mapping += [
|
||||
"summary_filename": "$id/qc/falco/${basename}_summary.txt",
|
||||
"report_filename": "$id/qc/falco/${basename}_fastqc_report.html",
|
||||
"data_filename": "$id/qc/falco/${basename}_fastqc_data.txt"
|
||||
]
|
||||
}
|
||||
return state_mapping
|
||||
},
|
||||
toState: { id, result, state ->
|
||||
// The output directory for all files above is the same:
|
||||
// take the directory from one of the files
|
||||
state + [ "output_sample_qc": result.html[0].parent ]
|
||||
state + [ "output_sample_qc" : result.outdir ]
|
||||
}
|
||||
)
|
||||
|
||||
| combine_samples.run(
|
||||
fromState: { id, state ->
|
||||
[
|
||||
|
||||
@@ -2,7 +2,7 @@ manifest {
|
||||
name = 'demultiplex'
|
||||
mainScript = 'main.nf'
|
||||
nextflowVersion = '!>=20.12.1-edge'
|
||||
version = 'v0.6.3'
|
||||
version = 'v0.6.4'
|
||||
description = 'Demultiplexing of raw sequencing data'
|
||||
}
|
||||
|
||||
|
||||
@@ -1,5 +1,5 @@
|
||||
name: "detect_demultiplexer"
|
||||
version: "v0.6.3"
|
||||
version: "v0.6.4"
|
||||
argument_groups:
|
||||
- name: "Arguments"
|
||||
arguments:
|
||||
@@ -168,11 +168,11 @@ build_info:
|
||||
output: "target/nextflow/detect_demultiplexer"
|
||||
executable: "target/nextflow/detect_demultiplexer/main.nf"
|
||||
viash_version: "0.9.4"
|
||||
git_commit: "459033886f31de68cf97477867ff26e27ae6d98e"
|
||||
git_commit: "dc228b2b4eebe9fe93fec86af537cf8211c3abec"
|
||||
git_remote: "https://github.com/viash-hub/demultiplex"
|
||||
package_config:
|
||||
name: "demultiplex"
|
||||
version: "v0.6.3"
|
||||
version: "v0.6.4"
|
||||
description: "Demultiplexing pipeline\n"
|
||||
info:
|
||||
test_resources:
|
||||
@@ -188,7 +188,7 @@ package_config:
|
||||
)'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'v0.6.3'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'v0.6.4'"
|
||||
keywords:
|
||||
- "bioinformatics"
|
||||
- "sequence"
|
||||
|
||||
@@ -1,5 +1,5 @@
|
||||
name: demultiplex
|
||||
version: v0.6.3
|
||||
version: v0.6.4
|
||||
description: |
|
||||
Demultiplexing pipeline
|
||||
license: MIT
|
||||
|
||||
@@ -1,4 +1,4 @@
|
||||
// detect_demultiplexer v0.6.3
|
||||
// detect_demultiplexer v0.6.4
|
||||
//
|
||||
// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
|
||||
// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
|
||||
@@ -3031,7 +3031,7 @@ meta = [
|
||||
"resources_dir": moduleDir.toRealPath().normalize(),
|
||||
"config": processConfig(readJsonBlob('''{
|
||||
"name" : "detect_demultiplexer",
|
||||
"version" : "v0.6.3",
|
||||
"version" : "v0.6.4",
|
||||
"argument_groups" : [
|
||||
{
|
||||
"name" : "Arguments",
|
||||
@@ -3224,12 +3224,12 @@ meta = [
|
||||
"engine" : "native|native",
|
||||
"output" : "target/nextflow/detect_demultiplexer",
|
||||
"viash_version" : "0.9.4",
|
||||
"git_commit" : "459033886f31de68cf97477867ff26e27ae6d98e",
|
||||
"git_commit" : "dc228b2b4eebe9fe93fec86af537cf8211c3abec",
|
||||
"git_remote" : "https://github.com/viash-hub/demultiplex"
|
||||
},
|
||||
"package_config" : {
|
||||
"name" : "demultiplex",
|
||||
"version" : "v0.6.3",
|
||||
"version" : "v0.6.4",
|
||||
"description" : "Demultiplexing pipeline\n",
|
||||
"info" : {
|
||||
"test_resources" : [
|
||||
@@ -3246,7 +3246,7 @@ meta = [
|
||||
".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
|
||||
".engines += { type: \\"native\\" }",
|
||||
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
|
||||
".engines[.type == 'docker'].target_tag := 'v0.6.3'"
|
||||
".engines[.type == 'docker'].target_tag := 'v0.6.4'"
|
||||
],
|
||||
"keywords" : [
|
||||
"bioinformatics",
|
||||
|
||||
@@ -2,7 +2,7 @@ manifest {
|
||||
name = 'detect_demultiplexer'
|
||||
mainScript = 'main.nf'
|
||||
nextflowVersion = '!>=20.12.1-edge'
|
||||
version = 'v0.6.3'
|
||||
version = 'v0.6.4'
|
||||
description = 'Detects the demultiplexer and accompanying sample information file which can be \nused to generate the fastq files.\n'
|
||||
}
|
||||
|
||||
|
||||
@@ -1,6 +1,6 @@
|
||||
name: "interop_summary_to_csv"
|
||||
namespace: "io"
|
||||
version: "v0.6.3"
|
||||
version: "v0.6.4"
|
||||
argument_groups:
|
||||
- name: "Input arguments"
|
||||
arguments:
|
||||
@@ -135,7 +135,7 @@ engines:
|
||||
id: "docker"
|
||||
image: "debian:stable-slim"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "v0.6.3"
|
||||
target_tag: "v0.6.4"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "apt"
|
||||
@@ -160,11 +160,11 @@ build_info:
|
||||
output: "target/nextflow/io/interop_summary_to_csv"
|
||||
executable: "target/nextflow/io/interop_summary_to_csv/main.nf"
|
||||
viash_version: "0.9.4"
|
||||
git_commit: "459033886f31de68cf97477867ff26e27ae6d98e"
|
||||
git_commit: "dc228b2b4eebe9fe93fec86af537cf8211c3abec"
|
||||
git_remote: "https://github.com/viash-hub/demultiplex"
|
||||
package_config:
|
||||
name: "demultiplex"
|
||||
version: "v0.6.3"
|
||||
version: "v0.6.4"
|
||||
description: "Demultiplexing pipeline\n"
|
||||
info:
|
||||
test_resources:
|
||||
@@ -180,7 +180,7 @@ package_config:
|
||||
)'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'v0.6.3'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'v0.6.4'"
|
||||
keywords:
|
||||
- "bioinformatics"
|
||||
- "sequence"
|
||||
|
||||
@@ -1,5 +1,5 @@
|
||||
name: demultiplex
|
||||
version: v0.6.3
|
||||
version: v0.6.4
|
||||
description: |
|
||||
Demultiplexing pipeline
|
||||
license: MIT
|
||||
|
||||
@@ -1,4 +1,4 @@
|
||||
// interop_summary_to_csv v0.6.3
|
||||
// interop_summary_to_csv v0.6.4
|
||||
//
|
||||
// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
|
||||
// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
|
||||
@@ -3032,7 +3032,7 @@ meta = [
|
||||
"config": processConfig(readJsonBlob('''{
|
||||
"name" : "interop_summary_to_csv",
|
||||
"namespace" : "io",
|
||||
"version" : "v0.6.3",
|
||||
"version" : "v0.6.4",
|
||||
"argument_groups" : [
|
||||
{
|
||||
"name" : "Input arguments",
|
||||
@@ -3203,7 +3203,7 @@ meta = [
|
||||
"id" : "docker",
|
||||
"image" : "debian:stable-slim",
|
||||
"target_registry" : "images.viash-hub.com",
|
||||
"target_tag" : "v0.6.3",
|
||||
"target_tag" : "v0.6.4",
|
||||
"namespace_separator" : "/",
|
||||
"setup" : [
|
||||
{
|
||||
@@ -3233,12 +3233,12 @@ meta = [
|
||||
"engine" : "docker|native",
|
||||
"output" : "target/nextflow/io/interop_summary_to_csv",
|
||||
"viash_version" : "0.9.4",
|
||||
"git_commit" : "459033886f31de68cf97477867ff26e27ae6d98e",
|
||||
"git_commit" : "dc228b2b4eebe9fe93fec86af537cf8211c3abec",
|
||||
"git_remote" : "https://github.com/viash-hub/demultiplex"
|
||||
},
|
||||
"package_config" : {
|
||||
"name" : "demultiplex",
|
||||
"version" : "v0.6.3",
|
||||
"version" : "v0.6.4",
|
||||
"description" : "Demultiplexing pipeline\n",
|
||||
"info" : {
|
||||
"test_resources" : [
|
||||
@@ -3255,7 +3255,7 @@ meta = [
|
||||
".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
|
||||
".engines += { type: \\"native\\" }",
|
||||
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
|
||||
".engines[.type == 'docker'].target_tag := 'v0.6.3'"
|
||||
".engines[.type == 'docker'].target_tag := 'v0.6.4'"
|
||||
],
|
||||
"keywords" : [
|
||||
"bioinformatics",
|
||||
@@ -3699,7 +3699,7 @@ meta["defaults"] = [
|
||||
"container" : {
|
||||
"registry" : "images.viash-hub.com",
|
||||
"image" : "vsh/demultiplex/io/interop_summary_to_csv",
|
||||
"tag" : "v0.6.3"
|
||||
"tag" : "v0.6.4"
|
||||
},
|
||||
"tag" : "$id"
|
||||
}'''),
|
||||
|
||||
@@ -2,7 +2,7 @@ manifest {
|
||||
name = 'io/interop_summary_to_csv'
|
||||
mainScript = 'main.nf'
|
||||
nextflowVersion = '!>=20.12.1-edge'
|
||||
version = 'v0.6.3'
|
||||
version = 'v0.6.4'
|
||||
}
|
||||
|
||||
process.container = 'nextflow/bash:latest'
|
||||
|
||||
@@ -1,6 +1,6 @@
|
||||
name: "publish"
|
||||
namespace: "io"
|
||||
version: "v0.6.3"
|
||||
version: "v0.6.4"
|
||||
argument_groups:
|
||||
- name: "Input arguments"
|
||||
arguments:
|
||||
@@ -204,7 +204,7 @@ engines:
|
||||
id: "docker"
|
||||
image: "debian:stable-slim"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "v0.6.3"
|
||||
target_tag: "v0.6.4"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "apt"
|
||||
@@ -222,11 +222,11 @@ build_info:
|
||||
output: "target/nextflow/io/publish"
|
||||
executable: "target/nextflow/io/publish/main.nf"
|
||||
viash_version: "0.9.4"
|
||||
git_commit: "459033886f31de68cf97477867ff26e27ae6d98e"
|
||||
git_commit: "dc228b2b4eebe9fe93fec86af537cf8211c3abec"
|
||||
git_remote: "https://github.com/viash-hub/demultiplex"
|
||||
package_config:
|
||||
name: "demultiplex"
|
||||
version: "v0.6.3"
|
||||
version: "v0.6.4"
|
||||
description: "Demultiplexing pipeline\n"
|
||||
info:
|
||||
test_resources:
|
||||
@@ -242,7 +242,7 @@ package_config:
|
||||
)'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'v0.6.3'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'v0.6.4'"
|
||||
keywords:
|
||||
- "bioinformatics"
|
||||
- "sequence"
|
||||
|
||||
@@ -1,5 +1,5 @@
|
||||
name: demultiplex
|
||||
version: v0.6.3
|
||||
version: v0.6.4
|
||||
description: |
|
||||
Demultiplexing pipeline
|
||||
license: MIT
|
||||
|
||||
@@ -1,4 +1,4 @@
|
||||
// publish v0.6.3
|
||||
// publish v0.6.4
|
||||
//
|
||||
// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
|
||||
// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
|
||||
@@ -3032,7 +3032,7 @@ meta = [
|
||||
"config": processConfig(readJsonBlob('''{
|
||||
"name" : "publish",
|
||||
"namespace" : "io",
|
||||
"version" : "v0.6.3",
|
||||
"version" : "v0.6.4",
|
||||
"argument_groups" : [
|
||||
{
|
||||
"name" : "Input arguments",
|
||||
@@ -3279,7 +3279,7 @@ meta = [
|
||||
"id" : "docker",
|
||||
"image" : "debian:stable-slim",
|
||||
"target_registry" : "images.viash-hub.com",
|
||||
"target_tag" : "v0.6.3",
|
||||
"target_tag" : "v0.6.4",
|
||||
"namespace_separator" : "/",
|
||||
"setup" : [
|
||||
{
|
||||
@@ -3302,12 +3302,12 @@ meta = [
|
||||
"engine" : "docker|native",
|
||||
"output" : "target/nextflow/io/publish",
|
||||
"viash_version" : "0.9.4",
|
||||
"git_commit" : "459033886f31de68cf97477867ff26e27ae6d98e",
|
||||
"git_commit" : "dc228b2b4eebe9fe93fec86af537cf8211c3abec",
|
||||
"git_remote" : "https://github.com/viash-hub/demultiplex"
|
||||
},
|
||||
"package_config" : {
|
||||
"name" : "demultiplex",
|
||||
"version" : "v0.6.3",
|
||||
"version" : "v0.6.4",
|
||||
"description" : "Demultiplexing pipeline\n",
|
||||
"info" : {
|
||||
"test_resources" : [
|
||||
@@ -3324,7 +3324,7 @@ meta = [
|
||||
".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
|
||||
".engines += { type: \\"native\\" }",
|
||||
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
|
||||
".engines[.type == 'docker'].target_tag := 'v0.6.3'"
|
||||
".engines[.type == 'docker'].target_tag := 'v0.6.4'"
|
||||
],
|
||||
"keywords" : [
|
||||
"bioinformatics",
|
||||
@@ -3404,7 +3404,7 @@ do
|
||||
mkdir -p \\$(dirname "\\$output_location") && echo "Containing directory \\$output_location created"
|
||||
|
||||
echo "Copying files..."
|
||||
cp -rL "\\$input_location" "\\$output_location"
|
||||
cp -a --keep-directory-symlink "\\$input_location" "\\$output_location"
|
||||
|
||||
echo "Output files for \\$output_location:"
|
||||
ls "\\$output_location"
|
||||
@@ -3415,7 +3415,7 @@ mkdir -p "\\$par_output_sample_qc"
|
||||
IFS=";" read -ra sample_qc_inputs <<< \\$par_input_sample_qc
|
||||
for qc_dir in "\\${sample_qc_inputs[@]}"; do
|
||||
echo "Copying contents of \\$qc_dir"
|
||||
find -H -D exec "\\$qc_dir" -type f -maxdepth 1 -exec cp -t "\\$par_output_sample_qc" {} +
|
||||
find -H -D exec "\\$qc_dir" -type f -maxdepth 1 -exec cp -a --keep-directory-symlink -t "\\$par_output_sample_qc" {} +
|
||||
done
|
||||
VIASHMAIN
|
||||
bash "$tempscript"
|
||||
@@ -3799,7 +3799,7 @@ meta["defaults"] = [
|
||||
"container" : {
|
||||
"registry" : "images.viash-hub.com",
|
||||
"image" : "vsh/demultiplex/io/publish",
|
||||
"tag" : "v0.6.3"
|
||||
"tag" : "v0.6.4"
|
||||
},
|
||||
"tag" : "$id"
|
||||
}'''),
|
||||
|
||||
@@ -2,7 +2,7 @@ manifest {
|
||||
name = 'io/publish'
|
||||
mainScript = 'main.nf'
|
||||
nextflowVersion = '!>=20.12.1-edge'
|
||||
version = 'v0.6.3'
|
||||
version = 'v0.6.4'
|
||||
description = 'Publish the processed results of the run'
|
||||
}
|
||||
|
||||
|
||||
@@ -1,6 +1,6 @@
|
||||
name: "untar"
|
||||
namespace: "io"
|
||||
version: "v0.6.3"
|
||||
version: "v0.6.4"
|
||||
argument_groups:
|
||||
- name: "Input arguments"
|
||||
arguments:
|
||||
@@ -141,7 +141,7 @@ engines:
|
||||
id: "docker"
|
||||
image: "debian:stable-slim"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "v0.6.3"
|
||||
target_tag: "v0.6.4"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "apt"
|
||||
@@ -159,11 +159,11 @@ build_info:
|
||||
output: "target/nextflow/io/untar"
|
||||
executable: "target/nextflow/io/untar/main.nf"
|
||||
viash_version: "0.9.4"
|
||||
git_commit: "459033886f31de68cf97477867ff26e27ae6d98e"
|
||||
git_commit: "dc228b2b4eebe9fe93fec86af537cf8211c3abec"
|
||||
git_remote: "https://github.com/viash-hub/demultiplex"
|
||||
package_config:
|
||||
name: "demultiplex"
|
||||
version: "v0.6.3"
|
||||
version: "v0.6.4"
|
||||
description: "Demultiplexing pipeline\n"
|
||||
info:
|
||||
test_resources:
|
||||
@@ -179,7 +179,7 @@ package_config:
|
||||
)'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'v0.6.3'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'v0.6.4'"
|
||||
keywords:
|
||||
- "bioinformatics"
|
||||
- "sequence"
|
||||
|
||||
@@ -1,5 +1,5 @@
|
||||
name: demultiplex
|
||||
version: v0.6.3
|
||||
version: v0.6.4
|
||||
description: |
|
||||
Demultiplexing pipeline
|
||||
license: MIT
|
||||
|
||||
@@ -1,4 +1,4 @@
|
||||
// untar v0.6.3
|
||||
// untar v0.6.4
|
||||
//
|
||||
// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
|
||||
// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
|
||||
@@ -3032,7 +3032,7 @@ meta = [
|
||||
"config": processConfig(readJsonBlob('''{
|
||||
"name" : "untar",
|
||||
"namespace" : "io",
|
||||
"version" : "v0.6.3",
|
||||
"version" : "v0.6.4",
|
||||
"argument_groups" : [
|
||||
{
|
||||
"name" : "Input arguments",
|
||||
@@ -3209,7 +3209,7 @@ meta = [
|
||||
"id" : "docker",
|
||||
"image" : "debian:stable-slim",
|
||||
"target_registry" : "images.viash-hub.com",
|
||||
"target_tag" : "v0.6.3",
|
||||
"target_tag" : "v0.6.4",
|
||||
"namespace_separator" : "/",
|
||||
"setup" : [
|
||||
{
|
||||
@@ -3232,12 +3232,12 @@ meta = [
|
||||
"engine" : "docker|native",
|
||||
"output" : "target/nextflow/io/untar",
|
||||
"viash_version" : "0.9.4",
|
||||
"git_commit" : "459033886f31de68cf97477867ff26e27ae6d98e",
|
||||
"git_commit" : "dc228b2b4eebe9fe93fec86af537cf8211c3abec",
|
||||
"git_remote" : "https://github.com/viash-hub/demultiplex"
|
||||
},
|
||||
"package_config" : {
|
||||
"name" : "demultiplex",
|
||||
"version" : "v0.6.3",
|
||||
"version" : "v0.6.4",
|
||||
"description" : "Demultiplexing pipeline\n",
|
||||
"info" : {
|
||||
"test_resources" : [
|
||||
@@ -3254,7 +3254,7 @@ meta = [
|
||||
".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
|
||||
".engines += { type: \\"native\\" }",
|
||||
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
|
||||
".engines[.type == 'docker'].target_tag := 'v0.6.3'"
|
||||
".engines[.type == 'docker'].target_tag := 'v0.6.4'"
|
||||
],
|
||||
"keywords" : [
|
||||
"bioinformatics",
|
||||
@@ -3728,7 +3728,7 @@ meta["defaults"] = [
|
||||
"container" : {
|
||||
"registry" : "images.viash-hub.com",
|
||||
"image" : "vsh/demultiplex/io/untar",
|
||||
"tag" : "v0.6.3"
|
||||
"tag" : "v0.6.4"
|
||||
},
|
||||
"tag" : "$id"
|
||||
}'''),
|
||||
|
||||
@@ -2,7 +2,7 @@ manifest {
|
||||
name = 'io/untar'
|
||||
mainScript = 'main.nf'
|
||||
nextflowVersion = '!>=20.12.1-edge'
|
||||
version = 'v0.6.3'
|
||||
version = 'v0.6.4'
|
||||
description = 'Unpack a .tar file. When the contents of the .tar file is just a single directory,\nput the contents of the directory into the output folder instead of that directory.\n'
|
||||
}
|
||||
|
||||
|
||||
@@ -1,5 +1,5 @@
|
||||
name: "runner"
|
||||
version: "v0.6.3"
|
||||
version: "v0.6.4"
|
||||
argument_groups:
|
||||
- name: "Input arguments"
|
||||
arguments:
|
||||
@@ -217,14 +217,14 @@ build_info:
|
||||
output: "target/nextflow/runner"
|
||||
executable: "target/nextflow/runner/main.nf"
|
||||
viash_version: "0.9.4"
|
||||
git_commit: "459033886f31de68cf97477867ff26e27ae6d98e"
|
||||
git_commit: "dc228b2b4eebe9fe93fec86af537cf8211c3abec"
|
||||
git_remote: "https://github.com/viash-hub/demultiplex"
|
||||
dependencies:
|
||||
- "target/nextflow/demultiplex"
|
||||
- "target/nextflow/io/publish"
|
||||
package_config:
|
||||
name: "demultiplex"
|
||||
version: "v0.6.3"
|
||||
version: "v0.6.4"
|
||||
description: "Demultiplexing pipeline\n"
|
||||
info:
|
||||
test_resources:
|
||||
@@ -240,7 +240,7 @@ package_config:
|
||||
)'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'v0.6.3'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'v0.6.4'"
|
||||
keywords:
|
||||
- "bioinformatics"
|
||||
- "sequence"
|
||||
|
||||
@@ -1,5 +1,5 @@
|
||||
name: demultiplex
|
||||
version: v0.6.3
|
||||
version: v0.6.4
|
||||
description: |
|
||||
Demultiplexing pipeline
|
||||
license: MIT
|
||||
|
||||
@@ -1,4 +1,4 @@
|
||||
// runner v0.6.3
|
||||
// runner v0.6.4
|
||||
//
|
||||
// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
|
||||
// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
|
||||
@@ -3031,7 +3031,7 @@ meta = [
|
||||
"resources_dir": moduleDir.toRealPath().normalize(),
|
||||
"config": processConfig(readJsonBlob('''{
|
||||
"name" : "runner",
|
||||
"version" : "v0.6.3",
|
||||
"version" : "v0.6.4",
|
||||
"argument_groups" : [
|
||||
{
|
||||
"name" : "Input arguments",
|
||||
@@ -3301,12 +3301,12 @@ meta = [
|
||||
"engine" : "native|native",
|
||||
"output" : "target/nextflow/runner",
|
||||
"viash_version" : "0.9.4",
|
||||
"git_commit" : "459033886f31de68cf97477867ff26e27ae6d98e",
|
||||
"git_commit" : "dc228b2b4eebe9fe93fec86af537cf8211c3abec",
|
||||
"git_remote" : "https://github.com/viash-hub/demultiplex"
|
||||
},
|
||||
"package_config" : {
|
||||
"name" : "demultiplex",
|
||||
"version" : "v0.6.3",
|
||||
"version" : "v0.6.4",
|
||||
"description" : "Demultiplexing pipeline\n",
|
||||
"info" : {
|
||||
"test_resources" : [
|
||||
@@ -3323,7 +3323,7 @@ meta = [
|
||||
".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script += 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
|
||||
".engines += { type: \\"native\\" }",
|
||||
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
|
||||
".engines[.type == 'docker'].target_tag := 'v0.6.3'"
|
||||
".engines[.type == 'docker'].target_tag := 'v0.6.4'"
|
||||
],
|
||||
"keywords" : [
|
||||
"bioinformatics",
|
||||
|
||||
@@ -2,7 +2,7 @@ manifest {
|
||||
name = 'runner'
|
||||
mainScript = 'main.nf'
|
||||
nextflowVersion = '!>=20.12.1-edge'
|
||||
version = 'v0.6.3'
|
||||
version = 'v0.6.4'
|
||||
description = 'Runner for demultiplexing of raw sequencing data'
|
||||
}
|
||||
|
||||
|
||||
Reference in New Issue
Block a user