Universc module update #3493
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Universc module update #3493
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Changes: - No longer hides logs so Nextflow can actually see them - No longer relies on meta objects for parameters - No longer supports single file input (which did not work) - No longer adds containerOptions to the process - Splits the output parameters into separate channels
SPPearce
reviewed
Oct 4, 2023
| --reference ${reference_name} \\ | ||
| --description ${sample_arg} \\ | ||
| --id ${meta.id} \\ | ||
| --read1 ${reads[0]} --read2 ${reads[1]} \\ |
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Can this be on the next line
Suggested change
| --read1 ${reads[0]} --read2 ${reads[1]} \\ | |
| --read1 ${reads[0]} \\ | |
| --read2 ${reads[1]} \\ |
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| # save log files | ||
| echo !! > sample-${meta.id}/outs/_invocation |
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!! stands for the last executed command
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do we need it? If someone wants to debug they can look into .command.sh
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Agreed. Trying to write around Nextflow is a major bugbear of mine.
| "--per-cell-data", | ||
| "--verbose", | ||
| ].join(" ").trim() | ||
| } | ||
| container = "nf-core/universc:1.2.5.1" |
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Why is the container being set in here still?
| container = "nf-core/universc:1.2.5.1" | ||
| } | ||
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| withName: CELLRANGER_MKGTF { | ||
| container = "nf-core/universc:1.2.5.1" |
| container = "nf-core/universc:1.2.5.1" | ||
| } | ||
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| withName: CELLRANGER_MKGTF { | ||
| container = "nf-core/universc:1.2.5.1" | ||
| } | ||
| withName: CELLRANGER_MKREF{ | ||
| container = "nf-core/universc:1.2.5.1" |
| mkdir -p "${meta.id}/" | ||
| mkdir -p "${meta.id}/SC_RNA_COUNTER_CS" | ||
| mkdir -p "${meta.id}/journal" | ||
| touch ${meta.id}/_log.txt |
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Is this log file still being made?
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PR checklist
versions.ymlfile.labelPROFILE=docker pytest --tag <MODULE> --symlink --keep-workflow-wd --git-awarePROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd --git-awarePROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware