Closed glichtenstein closed 3 months ago
master
branch :x:base
to dev
Hi @glichtenstein,
It looks like this pull-request is has been made against the glichtenstein/demultiplex master
branch.
The master
branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master
are only allowed if they come from the glichtenstein/demultiplex dev
branch.
You do not need to close this PR, you can change the target branch to dev
by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.
Thanks again for your contribution!
nf-core lint
overall result: Passed :white_check_mark: :warning:Posted for pipeline commit c12458d
+| ✅ 182 tests passed |+
#| ❔ 3 tests were ignored |#
!| ❗ 6 tests had warnings |!
It will need the the nf-core/modules PR counterpart to pass the tests. https://github.com/nf-core/modules/pull/5638
Will close it in favor of https://github.com/nf-core/modules/pull/5734 with help of @k1sauce refactoring of demultiplex.nf
Closes https://github.com/nf-core/modules/issues/5612 nf-core/modules PR counterpart: https://github.com/nf-core/modules/pull/5638
PR checklist
nf-core lint
).nextflow run . -profile test,docker --outdir <OUTDIR>
).nextflow run . -profile debug,test,docker --outdir <OUTDIR>
).docs/usage.md
is updated.docs/output.md
is updated.CHANGELOG.md
is updated.README.md
is updated (including new tool citations and authors/contributors).Description
This pull request adds the optional parameter
--log_skipped_fastqs
to thedemultiplex
pipeline. This change was necessary to address the issue with logging skipped FASTQ files and preventing the AWS S3 issue.Patch Details
The changes in this PR were applied using a patch from a specific commit in the
nf-core/modules
repository. The commit details are as follows:git format-patch -1 22bc6c5b186e16432e5b82d1932020b9c92e7040 -o /<some_dir>/patch/
The patch was applied to ensure that the
demultiplex
repository includes the latest changes fromnf-core/modules
necessary for this feature.Testing
true
nextflow run glichtenstein/demultiplex -r 7d9538e --input nf-core-samplesheet.csv --outdir /data/scratch/iseq-DI/output -profile docker -work-dir /data/scratch/iseq-DI/workdir -resume --skip_tools fastp --log_empty_fastqs=true
falsenextflow run glichtenstein/demultiplex -r 7d9538e --input nf-core-samplesheet.csv --outdir /data/scratch/iseq-DI/output -profile docker -work-dir /data/scratch/iseq-DI/workdir -resume --skip_tools fastp --log_empty_fastqs=false
executor > local (5) [1a/e1ae22] process > NFCORE_DEMULTIPLEX:DEMULTIPLEX:BCL_DEMULTIPLEX:BCLCONVERT [100%] 1 of 1 ✔ [5f/05036f] process > NFCORE_DEMULTIPLEX:DEMULTIPLEX:FALCO (iseq-DI_S1_L001) [100%] 1 of 1 ✔ [84/64923f] process > NFCORE_DEMULTIPLEX:DEMULTIPLEX:MD5SUM (iseq-DI_S1_L001) [100%] 2 of 2 ✔ [11/351698] process > NFCORE_DEMULTIPLEX:DEMULTIPLEX:MULTIQC [100%] 1 of 1 ✔ -[nf-core/demultiplex] Pipeline completed successfully-
cat output/empty_fastqs.log
Empty or invalid FASTQ file: /data/scratch/iseq-DI/workdir/1a/e1ae22.../Bad-iseq-DI_S2_L001_R1_001.fastq.gz Empty or invalid FASTQ file: /data/scratch/iseq-DI/workdir/1a/e1ae22.../Bad-iseq-DI_S2_L001_R2_001.fastq.gzDataset used
SampleSheet was modified to include bad barcodes.
nf-core_samplesheet.csv
bcl_convert_samplesheet.csv