Closed jbv2 closed 1 month ago
nf-core lint
overall result: Passed :white_check_mark: :warning:Posted for pipeline commit 81784cb
+| ✅ 342 tests passed |+
#| ❔ 1 tests were ignored |#
!| ❗ 22 tests had warnings |!
Remaining TODOs:
--fastsa_largeref
are fixed #1080 )TODOs:
[x] Rename mapping_circularmapper_elongatedfai
to mapping_circularmapper_elongatedindex
as it is a BWA index and NOT a fai.
NOTE: Actually renamed circularmapper parameters to fasta_*
when they pertain to reference elongation. This is because a) they go in the reference sheet and b) their output publishing is also tied to save_reference
.
TODO:
@nf-core-bot fix linting
❎ Adding the circularfilter
parameter causes length filtering in the BAM_FILTERING step to fail. unsure what that is about.
Also: Due to how the CIRCULARMAPPER_CIRCULARGENERATOR
module is set up, it can currently only handle fasta files with the fasta
suffix, while fa
, and gzipped variants fail. (Unclear if gz
should be allowed in the module to begin with, but fa
should definitely work.
I attempted to tweak bin/filter_bam_fragment_length.py
to deactivate the check for @SQ
tags in the header of the input. This creates errors downstream, since the @SQ
tag does not get reintroduced, and is required for the NFCORE_EAGER:EAGER:SAMTOOLS_VIEW_GENOME
process. >.<
UPDATE: Found the problem. RealignSAMFile implicitly requires an additional input file that is a list of the circularised chromosomes. This is output by CircularGenerator, but was not picked up by the module. Need to update both modules to account for this extra file. In the presence of this file, RealignSAMFile will remove all @SQ
entries in the header EXCEPT those in the file.
https://github.com/nf-core/modules/pull/6131
Updated to the new CM modules, and added passing of the elongated chromosome list to RealignSAMFile.
New problem: When the extended reference is provided, CircularGenerator is not run, so no elongated chromosome list exists to go into mapping...
Need to generate that from the circulartarget and pass it on. Alternatively, adding an ifEmpty{ [] }
to the RealignSAMFile channel would work, but would break when circularfilter is used, as before.
random thought: Check that Circularmapper does what it's supposed to in the absence of the elongated chromosome file
Added some channel magic to create a file with the circular target info required by RealignSAMFile if an elongated reference is required. To go with the above, made a circular target required for CM, regardless of if an elongated fasta was provided.
Closes #1033 Linked to #921
PR checklist
scrape_software_versions.py
nf-core lint .
).nextflow run . -profile test,docker
).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).