Dev -> Master for 1.1.0 release #86
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add subway map
Workflow updates
Enable instititutional configs
…-skip-tools
By default fastp and falco are always skipped even without providing skip_tools options. After this change, skip_tools worked as expected i.e: --skip_tools fastp.
However there is still a problem with --trim_fastq true
No such variable: Exception evaluating property 'fastq' for nextflow.script.ChannelOut, Reason: groovy.lang.MissingPropertyException: No such property: fastq for class: groovyx.gpars.dataflow.DataflowBroadcast
-- Check script './workflows/demultiplex.nf' at line: 155
Problematic lines
if (trim_fastq) {
ch_fastq_to_qc = FASTP.out.fastq
}
This closes #82
nf-core modules update
Important! Template update for nf-core/tools v2.7.2
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matthdsm
approved these changes
Jan 23, 2023
maxulysse
reviewed
Jan 23, 2023
maxulysse
reviewed
Jan 23, 2023
| @@ -31,7 +31,7 @@ DDMMYY_SERIAL_NUMBER_FC3,/path/to/SampleSheet3.csv,3,/path/to/sequencer/output3 | |||
| | `lane` | Optional lane number. When a lane number is provided, only the given lane will be demultiplexed | | |||
| | `run_dir` | Full path to the Illumina sequencer output directory or a `tar.gz` file containing the contents of said directory | | |||
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| An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline. | |||
| An [example samplesheet](../assets/inputs/flowcell_input.csv) has been provided with the pipeline. | |||
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I'd recommend to version the flowcell_input.csv
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It should always point to the correct branch when someone is viewing the docs, right?
maxulysse
reviewed
Jan 23, 2023
maxulysse
reviewed
Jan 23, 2023
maxulysse
reviewed
Jan 23, 2023
adamrtalbot
approved these changes
Jan 23, 2023
Comment on lines
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| switch (demultiplexer) { | ||
| case ['bclconvert', 'bcl2fastq']: | ||
| // SUBWORKFLOW: illumina | ||
| // Runs when "demultiplexer" is set to "bclconvert" or "bcl2fastq" | ||
| BCL_DEMULTIPLEX( ch_flowcells, demultiplexer ) | ||
| ch_raw_fastq = ch_raw_fastq.mix( BCL_DEMULTIPLEX.out.fastq ) | ||
| ch_multiqc_files = ch_multiqc_files.mix( BCL_DEMULTIPLEX.out.reports.map { meta, report -> return report} ) | ||
| ch_multiqc_files = ch_multiqc_files.mix( BCL_DEMULTIPLEX.out.stats.map { meta, stats -> return stats } ) | ||
| ch_versions = ch_versions.mix(BCL_DEMULTIPLEX.out.versions) | ||
| break | ||
| case 'bases2fastq': | ||
| // MODULE: bases2fastq | ||
| // Runs when "demultiplexer" is set to "bases2fastq" | ||
| BASES_DEMULTIPLEX ( ch_flowcells ) | ||
| ch_raw_fastq = ch_raw_fastq.mix(BASES_DEMULTIPLEX.out.fastq) | ||
| // TODO: verify that this is the correct output | ||
| ch_multiqc_files = ch_multiqc_files.mix(BASES_DEMULTIPLEX.out.metrics.map { meta, metrics -> return metrics} ) | ||
| ch_versions = ch_versions.mix(BASES_DEMULTIPLEX.out.versions) | ||
| break | ||
| default: | ||
| exit 1, "Unknown demultiplexer: ${demultiplexer}" | ||
| } |
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😊 Much more readable than messing with ext.when IMO
| FASTP(ch_raw_fastq, [], []) | ||
| ch_multiqc_files = ch_multiqc_files.mix( FASTP.out.json.map { meta, json -> return json} ) | ||
| ch_versions = ch_versions.mix(FASTP.out.versions) | ||
| if (!("fastp" in skip_tools)){ |
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"If not tool in skip_tools" is pretty convoluted, but I can't quite work out an easier way of doing it. "Unless tool in skip_tools?"
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It's less code to wrap this way. I think if it had the python syntax, and you could say if "fastp" not in skip_tools it might be easier to read.
@matthdsm wrote that bit.
Also adds two blank lines
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