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fix macrel faa input #242

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merged 10 commits into from
Apr 14, 2023
Merged

fix macrel faa input #242

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98a0815
Merge pull request #231 from nf-core/dev
jasmezz Feb 27, 2023
7b32bd6
fix macrel faa input
Darcy220606 Mar 8, 2023
b965e86
added the changes to changelog.md
Darcy220606 Mar 8, 2023
8ad1cda
Merge branch 'dev' into fix_macrel_faa
jfy133 Mar 17, 2023
c8ca2b7
Merge branch 'nf-core:master' into fix_macrel_faa
Darcy220606 Mar 29, 2023
55240a5
Merge branch 'dev' into fix_macrel_faa
Darcy220606 Mar 29, 2023
75b32b8
Bump macrel version to 1.2.0
Darcy220606 Apr 5, 2023
749dac6
harshels alignments in amp.nf :)
Darcy220606 Apr 5, 2023
23197b3
Update changelog with macrel version
Darcy220606 Apr 13, 2023
6b34f55
Update CHANGELOG.md
Darcy220606 Apr 13, 2023
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -16,6 +16,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#237](https://github.com/nf-core/funcscan/pull/237) Reactivate DeepARG automatic database downloading and CI tests as server is now back up. (by @jfy133)
- [#235](https://github.com/nf-core/funcscan/pull/235) Improved annotation speed by switching off pipeline-irrelevant Bakta annotation steps by default. (by @jasmezz)
- [#235](https://github.com/nf-core/funcscan/pull/235) Renamed parameter `annotation_bakta_db` to `annotation_bakta_db_localpath`. (by @jasmezz)
- [#242](https://github.com/nf-core/funcscan/pull/242) Fixed MACREL '.faa' issue that was generated when it was run on its own. (by @Darcy220606)
- [#248](https://github.com/nf-core/funcscan/pull/248) Applied best-practice `error("message")` to all (sub)workflow files. (by @jasmezz)

### `Dependencies`
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2 changes: 1 addition & 1 deletion modules.json
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Expand Up @@ -143,7 +143,7 @@
},
"macrel/contigs": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "a5a5bb12e7cc25658fdc97d810f2d6688cdae169",
"installed_by": ["modules"]
},
"multiqc": {
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6 changes: 3 additions & 3 deletions modules/nf-core/macrel/contigs/main.nf
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24 changes: 14 additions & 10 deletions subworkflows/local/amp.nf
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Expand Up @@ -8,10 +8,9 @@ include { AMPLIFY_PREDICT } from '../.
include { AMPIR } from '../../modules/nf-core/ampir/main'
include { DRAMP_DOWNLOAD } from '../../modules/local/dramp_download'
include { AMPCOMBI } from '../../modules/nf-core/ampcombi/main'
include { GUNZIP as GUNZIP_MACREL ; GUNZIP as GUNZIP_HMMER } from '../../modules/nf-core/gunzip/main'
include { GUNZIP as GUNZIP_MACREL_PRED ; GUNZIP as GUNZIP_HMMER ; GUNZIP as GUNZIP_MACREL_ORFS } from '../../modules/nf-core/gunzip/main'
include { TABIX_BGZIP } from '../../modules/nf-core/tabix/bgzip/main'


workflow AMP {
take:
contigs // tuple val(meta), path(contigs)
Expand All @@ -21,6 +20,7 @@ workflow AMP {
ch_versions = Channel.empty()
ch_ampresults_for_ampcombi = Channel.empty()
ch_ampcombi_summaries = Channel.empty()
ch_macrel_faa = Channel.empty()

// When adding new tool that requires FAA, make sure to update conditions
// in funcscan.nf around annotation and AMP subworkflow execution
Expand All @@ -33,24 +33,28 @@ workflow AMP {
// AMPLIFY
if ( !params.amp_skip_amplify ) {
AMPLIFY_PREDICT ( ch_faa_for_amplify, [] )
ch_versions = ch_versions.mix(AMPLIFY_PREDICT.out.versions)
ch_ampresults_for_ampcombi = ch_ampresults_for_ampcombi.mix(AMPLIFY_PREDICT.out.tsv)
ch_versions = ch_versions.mix(AMPLIFY_PREDICT.out.versions)
ch_ampresults_for_ampcombi = ch_ampresults_for_ampcombi.mix(AMPLIFY_PREDICT.out.tsv)
}

// MACREL
if ( !params.amp_skip_macrel ) {
MACREL_CONTIGS ( contigs )
ch_versions = ch_versions.mix(MACREL_CONTIGS.out.versions)
GUNZIP_MACREL ( MACREL_CONTIGS.out.amp_prediction )
ch_versions = ch_versions.mix(GUNZIP_MACREL.out.versions)
ch_ampresults_for_ampcombi = ch_ampresults_for_ampcombi.mix(GUNZIP_MACREL.out.gunzip)
ch_versions = ch_versions.mix(MACREL_CONTIGS.out.versions)
GUNZIP_MACREL_PRED ( MACREL_CONTIGS.out.amp_prediction )
GUNZIP_MACREL_ORFS ( MACREL_CONTIGS.out.all_orfs )
ch_versions = ch_versions.mix(GUNZIP_MACREL_PRED.out.versions)
ch_versions = ch_versions.mix(GUNZIP_MACREL_ORFS.out.versions)
ch_ampresults_for_ampcombi = ch_ampresults_for_ampcombi.mix(GUNZIP_MACREL_PRED.out.gunzip)
ch_macrel_faa = ch_macrel_faa.mix(GUNZIP_MACREL_ORFS.out.gunzip)
ch_faa_for_ampcombi = ch_faa_for_ampcombi.mix(ch_macrel_faa)
}

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// AMPIR
if ( !params.amp_skip_ampir ) {
AMPIR ( ch_faa_for_ampir, params.amp_ampir_model, params.amp_ampir_minlength, 0.0 )
ch_versions = ch_versions.mix(AMPIR.out.versions)
ch_ampresults_for_ampcombi = ch_ampresults_for_ampcombi.mix(AMPIR.out.amps_tsv)
ch_versions = ch_versions.mix(AMPIR.out.versions)
ch_ampresults_for_ampcombi = ch_ampresults_for_ampcombi.mix(AMPIR.out.amps_tsv)
}

// HMMSEARCH
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