Add go-slim modules (generate_gaf and summarise_goslims) #72
Conversation
KateSakharova
left a comment
KateSakharova
left a comment
There was a problem hiding this comment.
Looks good!
I just left questions about understanding.
| @@ -0,0 +1,52 @@ | |||
|
|
|||
| process SUMMARISEGOSLIMS { | |||
There was a problem hiding this comment.
should it be summarisEDgoslims or summariZegoslims? (my english is far from ideal, ignore me if I'm saying rubbish)
There was a problem hiding this comment.
summarise is british and summarize american, so both are correct 😄
| @@ -0,0 +1,44 @@ | |||
|
|
|||
| process GENERATEGAF { | |||
There was a problem hiding this comment.
is it allowed to use _ in names in nf-core standards? I think better separate words for understanding..
There was a problem hiding this comment.
not allowed unfortunately, nf-core modules create yells at you if you try to include _ in module names
| --- | ||
| # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json | ||
| name: "generategaf" | ||
| description: Script that generates a GO Annotation File (GAF) out of an InterProScan result tsv file. |
There was a problem hiding this comment.
GAF is official name? should it be GOAF? (I think inclusion of GO brings more understanding)
There was a problem hiding this comment.
Yeah GAF is the official name: https://geneontology.org/docs/go-annotation-file-gaf-format-2.1/
mberacochea
left a comment
mberacochea
left a comment
There was a problem hiding this comment.
Hey, thanks @chrisAta . I left a couple of minor comments, other than that it looks good to me
| @@ -0,0 +1,200 @@ | |||
| protein_accession sequence_md5_digest sequence_length analysis signature_accession signature_description start_location stop_location score status date accession description go pathways_annotations | |||
| ERZ477576.7-NODE-7-length-64890-cov-13.9479_16 9a765c7e2dcc1fd002ad18ce661605dc 525 TIGRFAM TIGR01972 NDH_I_M: proton-translocating NADH-quinone oxidoreductase, chain M 13 520 1.1E-160 T 29-10-2019 IPR010227 NADH-quinone oxidoreductase, chain M/4 GO:0008137|GO:0042773|GO:0055114 Reactome: R-HSA-611105|Reactome: R-HSA-6799198 | |||
There was a problem hiding this comment.
Can you use the gaf module tests files?
Thes two will be used with the owltools module from #71 to make a GO-slim generation subworkflow after this PR