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Dev #304

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merged 4 commits into from
Oct 15, 2023
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Dev #304

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214083d
changes in the CHANGELOG.md
ypriverol Oct 14, 2023
063bc9f
change percolator
ypriverol Oct 14, 2023
eeab2b8
replace openms by thirdparty openms
ypriverol Oct 14, 2023
233bcb1
replace openms by thirdparty openms also for containers
ypriverol Oct 15, 2023
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20 changes: 19 additions & 1 deletion CHANGELOG.md
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Expand Up @@ -7,18 +7,36 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Added`

- [#275 BigBio](https://github.com/bigbio/quantms/pull/275) Added support for bruker data. And speed-up to DIA-NN pipeline.
- [#275 BigBio](https://github.com/bigbio/quantms/pull/275) Added support for bruker data.
- [#275 BigBio](https://github.com/bigbio/quantms/pull/275) And speed-up to DIA-NN pipeline.
- [#275 BigBio](https://github.com/bigbio/quantms/pull/275) Support for library-base search in DIA-NN pipeline.
- [#300 BigBio](https://github.com/bigbio/quantms/pull/300) Major refactoring of LFQ-DDA MBR algorithm.
- [#279 BigBio](https://github.com/bigbio/quantms/pull/279) Support for SAGE search engine.

### `Changed`

- Update for pmultiqc to pmultiqc=0.0.21
- Update for openms to openms=3.1.0
- Update for sdrf-pipelines to sdrf-pipelines=0.0.24
- Update for msstats to msstats=4.2.1

### `Fixed`

- Fixed bug where modification masses were not calculated correctly in DIA-NN conversion.
- Fixed multiple bugs Pull Request [#293 BigBio](https://github.com/bigbio/quantms/pull/293), [#279 BigBio](https://github.com/bigbio/quantms/pull/279), [#265 BigBio](https://github.com/bigbio/quantms/pull/265), [#260 BigBio](https://github.com/bigbio/quantms/pull/260), [#257 BigBio](https://github.com/bigbio/quantms/pull/257)

### `Dependencies`

- New dependency on `sage` search engine.

### `Parameters`

- feature_with_id_min_score: Minimum score of a feature with a peptide identification (default: 0.10)
- feature_without_id_min_score: Minimum score of a feature without peptide identification (transfer feature, default: 0.75)
- lfq_intensity_threshold: Minimum intensity of a feature to be considered in the MBR algorithm (default: 1000)
- sage_processes: Number of processes to use in SAGE search engine (default: 1)
- diann_speclib: Path to the spectral library to use in DIA-NN (default: null)

### `Deprecations`

## [1.1.1] nfcore/quantms - [03/27/23] - Berlin-Bern
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6 changes: 3 additions & 3 deletions modules/local/openms/consensusid/main.nf
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Expand Up @@ -3,10 +3,10 @@ process CONSENSUSID {
label 'process_single'
label 'openms'

conda "bioconda::openms=2.9.1"
conda "bioconda::openms-thirdparty=3.0.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms:2.9.1--h135471a_0' :
'biocontainers/openms:2.9.1--h135471a_0' }"
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.0.0--h9ee0642_1' :
'biocontainers/openms-thirdparty:3.0.0--h9ee0642_1' }"

input:
tuple val(meta), path(id_file), val(qval_score)
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6 changes: 3 additions & 3 deletions modules/local/openms/decoydatabase/main.nf
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Expand Up @@ -2,10 +2,10 @@ process DECOYDATABASE {
label 'process_very_low'
label 'openms'

conda "bioconda::openms=2.9.1"
conda "bioconda::openms-thirdparty=3.0.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms:2.9.1--h135471a_0' :
'biocontainers/openms:2.9.1--h135471a_0' }"
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.0.0--h9ee0642_1' :
'biocontainers/openms-thirdparty:3.0.0--h9ee0642_1' }"

input:
path(db_for_decoy)
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6 changes: 3 additions & 3 deletions modules/local/openms/epifany/main.nf
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Expand Up @@ -2,10 +2,10 @@ process EPIFANY {
label 'process_medium'
label 'openms'

conda "bioconda::openms=2.9.1"
conda "bioconda::openms-thirdparty=3.0.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms:2.9.1--h135471a_0' :
'biocontainers/openms:2.9.1--h135471a_0' }"
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.0.0--h9ee0642_1' :
'biocontainers/openms-thirdparty:3.0.0--h9ee0642_1' }"

input:
tuple val(meta), path(consus_file)
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6 changes: 3 additions & 3 deletions modules/local/openms/extractpsmfeatures/main.nf
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Expand Up @@ -4,10 +4,10 @@ process EXTRACTPSMFEATURES {
label 'process_single'
label 'openms'

conda "bioconda::openms=2.9.1"
conda "bioconda::openms-thirdparty=3.0.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms:2.9.1--h135471a_0' :
'biocontainers/openms:2.9.1--h135471a_0' }"
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.0.0--h9ee0642_1' :
'biocontainers/openms-thirdparty:3.0.0--h9ee0642_1' }"

input:
tuple val(meta), path(id_file)
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6 changes: 3 additions & 3 deletions modules/local/openms/falsediscoveryrate/main.nf
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Expand Up @@ -4,10 +4,10 @@ process FALSEDISCOVERYRATE {
label 'process_single'
label 'openms'

conda "bioconda::openms=2.9.1"
conda "bioconda::openms-thirdparty=3.0.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms:2.9.1--h135471a_0' :
'biocontainers/openms:2.9.1--h135471a_0' }"
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.0.0--h9ee0642_1' :
'biocontainers/openms-thirdparty:3.0.0--h9ee0642_1' }"

input:
tuple val(meta), path(id_file)
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6 changes: 3 additions & 3 deletions modules/local/openms/filemerge/main.nf
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Expand Up @@ -3,10 +3,10 @@ process FILEMERGE {
label 'process_single'
label 'openms'

conda "bioconda::openms=2.9.1"
conda "bioconda::openms-thirdparty=3.0.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms:2.9.1--h135471a_0' :
'biocontainers/openms:2.9.1--h135471a_0' }"
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.0.0--h9ee0642_1' :
'biocontainers/openms-thirdparty:3.0.0--h9ee0642_1' }"

input:
file(id_map)
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6 changes: 3 additions & 3 deletions modules/local/openms/idconflictresolver/main.nf
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Expand Up @@ -2,10 +2,10 @@ process IDCONFLICTRESOLVER {
label 'process_low'
label 'openms'

conda "bioconda::openms=2.9.1"
conda "bioconda::openms-thirdparty=3.0.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms:2.9.1--h135471a_0' :
'biocontainers/openms:2.9.1--h135471a_0' }"
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.0.0--h9ee0642_1' :
'biocontainers/openms-thirdparty:3.0.0--h9ee0642_1' }"

input:
path consus_file
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6 changes: 3 additions & 3 deletions modules/local/openms/idfilter/main.nf
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Expand Up @@ -4,10 +4,10 @@ process IDFILTER {
label 'process_single'
label 'openms'

conda "bioconda::openms=2.9.1"
conda "bioconda::openms-thirdparty=3.0.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms:2.9.1--h135471a_0' :
'biocontainers/openms:2.9.1--h135471a_0' }"
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.0.0--h9ee0642_1' :
'biocontainers/openms-thirdparty:3.0.0--h9ee0642_1' }"

input:
tuple val(meta), path(id_file)
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6 changes: 3 additions & 3 deletions modules/local/openms/idmapper/main.nf
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Expand Up @@ -3,10 +3,10 @@ process IDMAPPER {
label 'process_medium'
label 'openms'

conda "bioconda::openms=2.9.1"
conda "bioconda::openms-thirdparty=3.0.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms:2.9.1--h135471a_0' :
'biocontainers/openms:2.9.1--h135471a_0' }"
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.0.0--h9ee0642_1' :
'biocontainers/openms-thirdparty:3.0.0--h9ee0642_1' }"

input:
tuple val(meta), path(id_file), path(map_file)
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6 changes: 3 additions & 3 deletions modules/local/openms/idpep/main.nf
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Expand Up @@ -3,10 +3,10 @@ process IDPEP {
label 'process_very_low'
label 'openms'

conda "openms::openms-thirdparty=3.1.0"
conda "bioconda::openms-thirdparty=3.0.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'ghcr.io/openms/openms-executables-sif:latest' :
'ghcr.io/openms/openms-executables:latest' }"
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.0.0--h9ee0642_1' :
'biocontainers/openms-thirdparty:3.0.0--h9ee0642_1' }"

input:
tuple val(meta), path(id_file)
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6 changes: 3 additions & 3 deletions modules/local/openms/idscoreswitcher/main.nf
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Expand Up @@ -4,10 +4,10 @@ process IDSCORESWITCHER {
label 'process_single'
label 'openms'

conda "bioconda::openms=2.9.1"
conda "bioconda::openms-thirdparty=3.0.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms:2.9.1--h135471a_0' :
'biocontainers/openms:2.9.1--h135471a_0' }"
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.0.0--h9ee0642_1' :
'biocontainers/openms-thirdparty:3.0.0--h9ee0642_1' }"

input:
tuple val(meta), path(id_file), val(new_score)
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6 changes: 3 additions & 3 deletions modules/local/openms/indexpeptides/main.nf
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Expand Up @@ -3,10 +3,10 @@ process INDEXPEPTIDES {
label 'process_low'
label 'openms'

conda "bioconda::openms=2.9.1"
conda "bioconda::openms-thirdparty=3.0.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms:2.9.1--h135471a_0' :
'biocontainers/openms:2.9.1--h135471a_0' }"
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.0.0--h9ee0642_1' :
'biocontainers/openms-thirdparty:3.0.0--h9ee0642_1' }"

input:
tuple val(meta), path(id_file), path(database)
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6 changes: 3 additions & 3 deletions modules/local/openms/isobaricanalyzer/main.nf
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Expand Up @@ -3,10 +3,10 @@ process ISOBARICANALYZER {
label 'process_medium'
label 'openms'

conda "bioconda::openms=2.9.1"
conda "bioconda::openms-thirdparty=3.0.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms:2.9.1--h135471a_0' :
'biocontainers/openms:2.9.1--h135471a_0' }"
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.0.0--h9ee0642_1' :
'biocontainers/openms-thirdparty:3.0.0--h9ee0642_1' }"

input:
tuple val(meta), path(mzml_file)
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6 changes: 3 additions & 3 deletions modules/local/openms/msstatsconverter/main.nf
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Expand Up @@ -3,10 +3,10 @@ process MSSTATSCONVERTER {
label 'process_low'
label 'openms'

conda "bioconda::openms=2.9.1"
conda "bioconda::openms-thirdparty=3.0.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms:2.9.1--h135471a_0' :
'biocontainers/openms:2.9.1--h135471a_0' }"
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.0.0--h9ee0642_1' :
'biocontainers/openms-thirdparty:3.0.0--h9ee0642_1' }"

input:
path consensusXML
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6 changes: 3 additions & 3 deletions modules/local/openms/mzmlindexing/main.nf
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Expand Up @@ -3,10 +3,10 @@ process MZMLINDEXING {
label 'process_low'
label 'openms'

conda "bioconda::openms=2.9.1"
conda "bioconda::openms-thirdparty=3.0.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms:2.9.1--h135471a_0' :
'biocontainers/openms:2.9.1--h135471a_0' }"
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.0.0--h9ee0642_1' :
'biocontainers/openms-thirdparty:3.0.0--h9ee0642_1' }"

input:
tuple val(meta), path(mzmlfile)
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6 changes: 3 additions & 3 deletions modules/local/openms/openmspeakpicker/main.nf
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Expand Up @@ -3,10 +3,10 @@ process OPENMSPEAKPICKER {
label 'process_low'
label 'openms'

conda "bioconda::openms=2.9.1"
conda "bioconda::openms-thirdparty=3.0.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms:2.9.1--h135471a_0' :
'biocontainers/openms:2.9.1--h135471a_0' }"
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.0.0--h9ee0642_1' :
'biocontainers/openms-thirdparty:3.0.0--h9ee0642_1' }"

input:
tuple val(meta), path(mzml_file)
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6 changes: 3 additions & 3 deletions modules/local/openms/proteininference/main.nf
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Expand Up @@ -2,10 +2,10 @@ process PROTEININFERENCE {
label 'process_medium'
label 'openms'

conda "bioconda::openms=2.9.1"
conda "bioconda::openms-thirdparty=3.0.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms:2.9.1--h135471a_0' :
'biocontainers/openms:2.9.1--h135471a_0' }"
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.0.0--h9ee0642_1' :
'biocontainers/openms-thirdparty:3.0.0--h9ee0642_1' }"

input:
tuple val(meta), path(consus_file)
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6 changes: 3 additions & 3 deletions modules/local/openms/proteinquantifier/main.nf
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Expand Up @@ -3,10 +3,10 @@ process PROTEINQUANTIFIER {
label 'process_medium'
label 'openms'

conda "bioconda::openms=2.9.1"
conda "bioconda::openms-thirdparty=3.0.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms:2.9.1--h135471a_0' :
'biocontainers/openms:2.9.1--h135471a_0' }"
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.0.0--h9ee0642_1' :
'biocontainers/openms-thirdparty:3.0.0--h9ee0642_1' }"

input:
path epi_filt_resolve
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6 changes: 3 additions & 3 deletions modules/local/openms/proteomicslfq/main.nf
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Expand Up @@ -3,10 +3,10 @@ process PROTEOMICSLFQ {
label 'process_high'
label 'openms'

conda "bioconda::openms=2.9.1"
conda "bioconda::openms-thirdparty=3.0.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms:2.9.1--h135471a_0' :
'biocontainers/openms:2.9.1--h135471a_0' }"
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.0.0--h9ee0642_1' :
'biocontainers/openms-thirdparty:3.0.0--h9ee0642_1' }"

input:
path(mzmls)
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6 changes: 3 additions & 3 deletions modules/local/openms/thirdparty/percolator/main.nf
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Expand Up @@ -3,10 +3,10 @@ process PERCOLATOR {
label 'process_medium'
label 'openms'

conda "bioconda::openms=2.9.1"
conda "bioconda::openms-thirdparty=3.0.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms:2.9.1--h135471a_0' :
'biocontainers/openms:2.9.1--h135471a_0' }"
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.0.0--h9ee0642_1' :
'biocontainers/openms-thirdparty:3.0.0--h9ee0642_1' }"

input:
tuple val(meta), path(id_file)
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6 changes: 3 additions & 3 deletions modules/local/openms/thirdparty/searchenginecomet/main.nf
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Expand Up @@ -3,10 +3,10 @@ process SEARCHENGINECOMET {
label 'process_medium'
label 'openms'

conda "bioconda::openms=2.9.1"
conda "bioconda::openms-thirdparty=3.0.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms:2.9.1--h135471a_0' :
'biocontainers/openms:2.9.1--h135471a_0' }"
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.0.0--h9ee0642_1' :
'biocontainers/openms-thirdparty:3.0.0--h9ee0642_1' }"

input:
tuple val(meta), path(mzml_file), path(database)
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6 changes: 3 additions & 3 deletions modules/local/openms/thirdparty/searchenginesage/main.nf
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Expand Up @@ -3,10 +3,10 @@ process SEARCHENGINESAGE {
label 'process_medium' // we could make it dependent on the number of files
label 'openms'

conda "bioconda::openms=2.9.1"
conda "bioconda::openms-thirdparty=3.0.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms:2.9.1--h135471a_0' :
'biocontainers/openms:2.9.1--h135471a_0' }"
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.0.0--h9ee0642_1' :
'biocontainers/openms-thirdparty:3.0.0--h9ee0642_1' }"

input:
tuple val(key), val(batch), val(metas), path(mzml_files), path(database)
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