Closed priyanka-surana closed 1 year ago
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nf-core lint
overall result: Failed :x:Posted for pipeline commit d794912
+| ✅ 120 tests passed |+
#| ❔ 19 tests were ignored |#
!| ❗ 10 tests had warnings |!
-| ❌ 3 tests failed |-
nf-core lint
overall result: Failed :x:Posted for pipeline commit ff86cf4
+| ✅ 117 tests passed |+
#| ❔ 19 tests were ignored |#
!| ❗ 11 tests had warnings |!
-| ❌ 5 tests failed |-
@muffato Can you take a look at the docs/output.md
?
There are still params in subworkflows in 3 places as taking them out the subworkflow into the workflow isn't as simple as the others:
In blobtools.nf
params.accession
and params.yaml
from line 30 to 42
In busco_diamond_blastp.nf
there is params.taxon
and params.taxa_file
on line 37 and params.busco_lineages_path
on line 61
@muffato Can you take a look at the
docs/output.md
?
- Do we need all these files in the long term?
I see the "blobdir" as the most important output of BTK, and it will include coverage, BUSCO, etc, data, although in a BTK-specific JSON format. All the other files (outputs from fasta_windows, Busco, etc) are therefore intermediate files which I would probably not publish by default.
I would review that after the first one or two releases, when we start discussing how the yaml config file can be used to drive the pipeline. In the meantime, if anyone wants some extra outputs, they could add an extra config file with some publishDir
directives.
- Does the results folder structure make sense?
👍🏼 for blobdir/${meta.id}
There are still params in subworkflows in 3 places as taking them out the subworkflow into the workflow isn't as simple as the others:
In
blobtools.nf
params.accession
andparams.yaml
from line 30 to 42In
busco_diamond_blastp.nf
there isparams.taxon
andparams.taxa_file
on line 37 andparams.busco_lineages_path
on line 61
Possible solution for organizing parameters:
blastp_outext
and blastp_cols
, these are defined as input in diamond_blastp module and not as args
, so they are required only in nextflow.config and are not specified elsewhere.params.accession
, params.yaml
, params.taxon
and params.taxa_file
. Then each of these should be declared as input in each subworkflow where they appear (using take:
) and substituting each occurrence by the name declared after take:
.
Generic cleanup branch to start fixing the formatting issues.
PR checklist
nf-core lint
).nextflow run . -profile test,singularity,sanger --outdir <OUTDIR>
) locally.nextflow run . -profile test_full,singularity,sanger --outdir <OUTDIR>
) locally.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).