Closed Aratz closed 4 months ago
nf-core lint
overall result: Passed :white_check_mark: :warning:Posted for pipeline commit 8ac4d76
+| ✅ 174 tests passed |+
!| ❗ 21 tests had warnings |!
master
branch :x:base
to dev
Hi @Aratz,
It looks like this pull-request is has been made against the Aratz/seqinspector 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 Aratz/seqinspector 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!
Is this ready for review @Aratz ?
Not quite, the tests need fixing and I need to go through the rest of the PR checklist (but the code is there).
If I .dump()
the ch_samplesheet
, neither the id: nor the path to the FastQ file are quoted. Should they be strings, or is that intentional?
[DUMP: samplesheet] [['sample':'Sample1', 'lane':1, 'group':'S1', 'rundir':null, 'id':Sample1_S1_1, 'single_end':true], [/nf-core/test-datasets/raw/seqinspector/testdata/NovaSeq6000/200624_A00834_0183_BHMTFYDRXX/Sample1_S1_L001_R1_001.fastq.gz]]
[DUMP: samplesheet] [['sample':'SampleA', 'lane':1, 'group':'S2', 'rundir':null, 'id':SampleA_S2_1, 'single_end':true], [/nf-core/test-datasets/raw/seqinspector/testdata/NovaSeq6000/200624_A00834_0183_BHMTFYDRXX/SampleA_S2_L001_R1_001.fastq.gz]]
[DUMP: samplesheet] [['sample':'Sample23', 'lane':1, 'group':'S3', 'rundir':null, 'id':Sample23_S3_1, 'single_end':true], [/nf-core/test-datasets/raw/seqinspector/testdata/NovaSeq6000/200624_A00834_0183_BHMTFYDRXX/Sample23_S3_L001_R1_001.fastq.gz]]
[DUMP: samplesheet] [['sample':'sampletest', 'lane':1, 'group':'S4', 'rundir':null, 'id':sampletest_S4_1, 'single_end':true], [/nf-core/test-datasets/raw/seqinspector/testdata/NovaSeq6000/200624_A00834_0183_BHMTFYDRXX/sampletest_S4_L001_R1_001.fastq.gz]]
[DUMP: samplesheet] [['sample':'Undetermined', 'lane':1, 'group':null, 'rundir':null, 'id':Undetermined_ungrouped_1, 'single_end':true], [/nf-core/test-datasets/raw/seqinspector/testdata/NovaSeq6000/200624_A00834_0183_BHMTFYDRXX/Undetermined_S0_L001_R1_001.fastq.gz]]
If I
.dump()
thech_samplesheet
, neither the id: nor the path to the FastQ file are quoted. Should they be strings, or is that intentional?[DUMP: samplesheet] [['sample':'Sample1', 'lane':1, 'group':'S1', 'rundir':null, 'id':Sample1_S1_1, 'single_end':true], [/nf-core/test-datasets/raw/seqinspector/testdata/NovaSeq6000/200624_A00834_0183_BHMTFYDRXX/Sample1_S1_L001_R1_001.fastq.gz]] [DUMP: samplesheet] [['sample':'SampleA', 'lane':1, 'group':'S2', 'rundir':null, 'id':SampleA_S2_1, 'single_end':true], [/nf-core/test-datasets/raw/seqinspector/testdata/NovaSeq6000/200624_A00834_0183_BHMTFYDRXX/SampleA_S2_L001_R1_001.fastq.gz]] [DUMP: samplesheet] [['sample':'Sample23', 'lane':1, 'group':'S3', 'rundir':null, 'id':Sample23_S3_1, 'single_end':true], [/nf-core/test-datasets/raw/seqinspector/testdata/NovaSeq6000/200624_A00834_0183_BHMTFYDRXX/Sample23_S3_L001_R1_001.fastq.gz]] [DUMP: samplesheet] [['sample':'sampletest', 'lane':1, 'group':'S4', 'rundir':null, 'id':sampletest_S4_1, 'single_end':true], [/nf-core/test-datasets/raw/seqinspector/testdata/NovaSeq6000/200624_A00834_0183_BHMTFYDRXX/sampletest_S4_L001_R1_001.fastq.gz]] [DUMP: samplesheet] [['sample':'Undetermined', 'lane':1, 'group':null, 'rundir':null, 'id':Undetermined_ungrouped_1, 'single_end':true], [/nf-core/test-datasets/raw/seqinspector/testdata/NovaSeq6000/200624_A00834_0183_BHMTFYDRXX/Undetermined_S0_L001_R1_001.fastq.gz]]
I'm not certain but I think id
is not quoted because it's a GString
, and I think Path objects aren't quoted either as they're not strings
I'm not certain but I think
id
is not quoted because it's aGString
, and I think Path objects aren't quoted either as they're not strings
I see. I mainly noticed it, because I wanted to create a minimally reproducible example to try out that other pattern that I had in mind. Thus, I copy-pasted the dump into a single main.nf
script and used a Channel.of()
factory, and it would not work (and produced an extremely unhelpful error message) unless I quoted everything.
nf-test is not working for me since the last 3 commits, it seems params.pipelines_testdata_base_path
evaluates to null
edit: fixed in 4329bb9
nf-core lint
overall result: Passed :white_check_mark: :warning:Posted for pipeline commit 02affeb
+| ✅ 177 tests passed |+
!| ❗ 21 tests had warnings |!
I've tried to clean up the discussion thread and have pushed some additional commits to address simple issues. Requesting re-reviews.
I'll merge this now, thank you all for your reviews and comments. There are still some open discussions that I think are worth addressing but are not critical to this feature, we can keep discussing them here and in subsequent PRs.
This PR introduces MultiQC report generation by lane, by rundir and by sample group.
Closes #3
PR checklist
nf-core lint
).nf-test test main.nf.test -profile test,docker
).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).