Fix/prevent falco module to process an empty fastq file#5734
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glichtenstein wants to merge 79 commits intonf-core:5612-bcl-demultiplexfrom
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* port to nf-test * update tests to include versions
* Add missing tximport outputs * Update snapshot for tximeta/tximport
Replace multiple ifs with a single for The loop checks if files exist before moving them to temp/
* port to nf-test * update snap * update tests to include versions * port to nf-test * update snap * update tests to include versions * change snapshot to read the dict * check file md5sum * Apply suggestions from code review * update snap --------- Co-authored-by: Maxime U Garcia <maxime.garcia@seqera.io>
* port to nf-test * include versions in test * port to nf-test * include versions in test * change to check tables * change tests to assert whole output and update snap * generalize assertions
* add index * add bwameme_mem * Update modules/nf-core/bwameme/index/tests/main.nf.test Co-authored-by: Annick Renevey <47788523+rannick@users.noreply.github.com> --------- Co-authored-by: Annick Renevey <47788523+rannick@users.noreply.github.com>
* use conda-forge instead of anaconda * Update modules/nf-core/homer/maketagdirectory/environment.yml Co-authored-by: Phil Ewels <phil.ewels@seqera.io> * nf-test homer/findpeaks * nf-test homer/maketagdirectory * nf-test homer/pos2bed * fix perl version? * Update modules/nf-core/gawk/environment.yml Co-authored-by: Phil Ewels <phil.ewels@seqera.io> * fix gawk --------- Co-authored-by: Phil Ewels <phil.ewels@seqera.io>
The new container version no longer requires overriding the entrypoint.
* Added stub for sratools * Added command echo for fasterqdump
* Version bumped bwa/index and bwa/aln * Removed bam md5sum from snapshot
* Bump bwa mem version * Most recent htslib
* add mmseqs_contig_taxonomy * apply prettier * code linting * changed the test dataset to bacteroides_fragilis instead of influenzae * give more memory to mmseqs-taxa * memory increased to 16.GB * increase the process mem requirements * fix memory * add reviewer suggestion * change back memory * fix snap * fix snap
…-core#5598) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
…f-core#5636) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
* add rrnatransctipts * add util for extracting ribosomal transcripts * fix tests * fix tests * mixup with ucsc gtftogenepred * mixup with ucsc gtftogenepred * mixup with ucsc gtftogenepred * make output optional * fill meta * reset gtftogenepred * use grep instead of template * fix * fix test so if grep does not find anything, the exit code is still 0 --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
…ow (nf-core#5628) * Return primary bam and index file in fastq_align_bamcmp_bwa subworkflow and update snapshots. * Add new tests and update snapshots. * Remove opt out for conda for fastq_align_bamcmp_bwa * Update snapshots * Restore opt out for conda for fastq_align_bamcmp_bwa --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
* Author: @MartaSantanaSilva Initial pull for module grabix/check Addition of one test (total: 1) * Update modules/nf-core/grabix/check/main.nf Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * Update modules/nf-core/grabix/check/main.nf Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * Update modules/nf-core/grabix/check/main.nf Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * Update modules/nf-core/grabix/check/meta.yml Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * new module: grabix Fixes nf-core#5181 * Apply suggestions from code review * Update modules/nf-core/grabix/check/meta.yml * fix conda declaration * update snapshot * prettier --------- Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Co-authored-by: Maxime U Garcia <maxime.garcia@seqera.io> Co-authored-by: maxulysse <max.u.garcia@gmail.com>
Parabricks doesn't require stageInMode to be 'copy' Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>
* chore(deps): update biocontainers/glimpse-bio docker tag to v2.0.1 * Update main.nf * Update main.nf * Update main.nf * Update main.nf * Update main.nf * Update main.nf * Update main.nf * The channel was renamed in nf-core#5117 * The Conda yml files need to match the container definitions * Typo ! There was a missing s --------- Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Louis LE NEZET <58640615+LouisLeNezet@users.noreply.github.com> Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk>
…core#5653) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
* Bump csvtk new version * Add nf-test * Get rid of pytest * Bump version in singularity images * Update tests/config/pytest_modules.yml --------- Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
* Stub and nf-test for fastk/fastk * Added chmod +r to add read permissions for docker * Added a+r
* Remove leftover of previous PR * Bump version 0.30.0 of csvtk * Ad nf-test for csvtk/split * Remove csvtk/split from pytest_modules.yml * Make lint happy * Update path on tests * Update modules/nf-core/csvtk/split/tests/main.nf.test * Update modules/nf-core/csvtk/split/tests/main.nf.test
…f-core#5662) * Remove cp operation from bclconvert Replaces cp operation with native Nextflow output path handling. Fixes nf-core#5644 * Update modules/nf-core/bclconvert/main.nf
* working on the main.nf and meta.yml initially * working on the main.nf and meta.yml initially * Adding the updates to meta.yml * Adding the latest code changes that add a working version of the tests * Fixing the version mismatch in the docker and singularity containers * Removing the trailing whitespaces * Bump parabricks 4.3.0-1 + remove stageInMode (nf-core#5646) Parabricks doesn't require stageInMode to be 'copy' Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io> * glimpse2 version bump - abandoned (nf-core#4236) * chore(deps): update biocontainers/glimpse-bio docker tag to v2.0.1 * Update main.nf * Update main.nf * Update main.nf * Update main.nf * Update main.nf * Update main.nf * Update main.nf * The channel was renamed in nf-core#5117 * The Conda yml files need to match the container definitions * Typo ! There was a missing s --------- Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Louis LE NEZET <58640615+LouisLeNezet@users.noreply.github.com> Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk> * Update pre-commit hook renovatebot/pre-commit-hooks to v37.371.1 (nf-core#5653) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Bump csvtk version to CSVTK/JOIN and add nf-test (nf-core#5642) * Bump csvtk new version * Add nf-test * Get rid of pytest * Bump version in singularity images * Update tests/config/pytest_modules.yml --------- Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> * Added task.memory to meryl modules and .meryl ext for outputs (nf-core#5655) * Stub and nf-test for fastk/fastk (nf-core#5631) * Stub and nf-test for fastk/fastk * Added chmod +r to add read permissions for docker * Added a+r * Bump csvtk version to CSVTK/SPLIT and add nf-test (nf-core#5656) * Remove leftover of previous PR * Bump version 0.30.0 of csvtk * Ad nf-test for csvtk/split * Remove csvtk/split from pytest_modules.yml * Make lint happy * Update path on tests * Update modules/nf-core/csvtk/split/tests/main.nf.test * Update modules/nf-core/csvtk/split/tests/main.nf.test * Update modules/nf-core/viennarna/rnafold/tests/main.nf.test Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> * Adding the corrected version of meta.yml file --------- Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io> Co-authored-by: Marcel Ribeiro-Dantas <marcel.ribeirodantas@seqera.io> Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Louis LE NEZET <58640615+LouisLeNezet@users.noreply.github.com> Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk> Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Co-authored-by: Usman Rashid <usman@smme.edu.pk>
* Add nf-test to chromap/index * Updated snapshot and removed old tests * Fix chromap versions and add tags * [automated] Fix linting with Prettier * Check genome.index exists instead of match Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> * snapshot fix * Updated snapshot * Add version to snapshot * Change version to versions in snapshot --------- Co-authored-by: nf-core-bot <core@nf-co.re> Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
glichtenstein
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muffato
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CharlotteAnne,
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Merged
Contributor
|
@glichtenstein, I think your branch is very out of date. Can you please open a new PR with a clean history. |
Contributor
Author
I am so sorry, I synced the fork before the PR but I may have missed something. Thanks for taking care of it, I really appreciate it. |
Contributor
Author
|
new PR: #5769 |
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PR checklist
Closes #5612
@k1sauce What about doing the filter directly on the falco module main.nf. This way the subworkflow/bcl_demultiplex/main.nf does not have to handle this issue nor the workflow/demultiplex.nf
I have used a file size filter, to avoid inserting in the falco list of ${reads} those files that have less than 20bytes.
Rationale: An empty text file compressed in tar.gz is usually 20 bytes in size.
edited: /modules/nf-core/falco/main.nf#L20C1-L20C6
Closes #5638
versions.ymlfile.labelnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile condanf-core subworkflows test <SUBWORKFLOW> --profile dockernf-core subworkflows test <SUBWORKFLOW> --profile singularitynf-core subworkflows test <SUBWORKFLOW> --profile conda