Release v2.4.0 #256
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Release v2.4.0 #256
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See if this fixes the CI issue
…-multiqc fix (231): Null object accessed in multiqc channel
…llranger Fix_file_collision_when_using_cellranger
Update public_aws_ecr.config
Add singularity.registry = 'quay.io' and bump NF version to 23.04.0
Remove public_aws_ecr profile
Important! Template update for nf-core/tools v2.9
Update cellranger module
…tting Remove duplicate registry settings in nextflow.config
Add cellranger to multiqc report
fix typo causing empty version imformation for mtx_conversion subwork…
Bump version for release
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maxulysse
approved these changes
Aug 16, 2023
|
There is a missing |
|
Also, there is a missing support if the experiment is single-read for StarSolo. Here is my quick fix solution starting from here // separate forward from reverse pairs
def (forward, reverse) = reads.collate(2).transpose()
if (meta.single_end) {
forward = ''
reverse = reads.join( "," )
} else {
reverse = reverse.join( "," )
forward = forward.join( "," )
}
"""
STAR \\
--genomeDir $index \\
--readFilesIn $reverse $forward \\
--runThreadN $task.cpus \\
--outFileNamePrefix $prefix. \\
--soloCBwhitelist <(gzip -cdf $whitelist) \\
--soloType $protocol \\
--soloFeatures $star_feature \\
$other_10x_parameters \\
$out_sam_type \\
$ignore_gtf \\
$seq_center \\
$cell_filter \\
$args \\ |
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Hi @matq007, smart-seq is not a multiplexed experiment, you can process it with the |
I see, got it! |
fmalmeida
approved these changes
Aug 22, 2023
|
It seems that all is there. |
remove validationSchemaIgnoreParams warning with test profile
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PR checklist
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).