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Merge pull request #308 from ypriverol/dev
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Release of Openms 3.1.0
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@ypriverol
ypriverol authored Oct 21, 2023
2 parents 4163570 + 66ced37 commit 9786845
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Showing 26 changed files with 83 additions and 87 deletions.
24 changes: 10 additions & 14 deletions bin/diann_convert.py
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Expand Up @@ -97,7 +97,6 @@ def convert(ctx, folder, exp_design, dia_params, diann_version, charge, missed_c
out_msstats["Reference"] = out_msstats["Reference"].map(unique_reference_map)
del unique_reference_map

# TODO remove this if not debugging
logger.debug("\n\nReference Column >>>")
logger.debug(out_msstats["Reference"])

Expand All @@ -109,30 +108,27 @@ def convert(ctx, folder, exp_design, dia_params, diann_version, charge, missed_c

logger.debug(f"\n\ns_DataFrame ({s_DataFrame.shape})>>>")
logger.debug(s_DataFrame.head(5))
## END TODO

logger.debug("Adding Fraction, BioReplicate, Condition columns")
# Changing implementation from apply to merge went from several minutes to
# ~50ms
tmp = (
s_DataFrame[["Sample", "MSstats_Condition", "MSstats_BioReplicate"]]
.merge(f_table[["Fraction", "Sample", "run"]], on="Sample")
.rename(columns={"run": "Run", "MSstats_BioReplicate": "BioReplicate", "MSstats_Condition": "Condition"})
.drop(columns=["Sample"])
)
out_msstats = out_msstats.merge(
tmp,
(
s_DataFrame[["Sample", "MSstats_Condition", "MSstats_BioReplicate"]]
.merge(f_table[["Fraction", "Sample", "run"]], on="Sample")
.rename(columns={"run": "Run", "MSstats_BioReplicate": "BioReplicate", "MSstats_Condition": "Condition"})
.drop(columns=["Sample"])
),
on="Run",
validate="many_to_one",
)
del tmp
exp_out_prefix = str(Path(exp_design).stem)
exp_out_prefix = Path(exp_design).stem
out_msstats.to_csv(exp_out_prefix + "_msstats_in.csv", sep=",", index=False)
logger.info(f"MSstats input file is saved as {exp_out_prefix}_msstats_in.csv")

# Convert to Triqler
trinqler_cols = ["ProteinName", "PeptideSequence", "PrecursorCharge", "Intensity", "Run", "Condition"]
out_triqler = out_msstats[trinqler_cols]
triqler_cols = ["ProteinName", "PeptideSequence", "PrecursorCharge", "Intensity", "Run", "Condition"]
out_triqler = out_msstats[triqler_cols]
del out_msstats
out_triqler.columns = ["proteins", "peptide", "charge", "intensity", "run", "condition"]
out_triqler = out_triqler[out_triqler["intensity"] != 0]
Expand All @@ -143,7 +139,7 @@ def convert(ctx, folder, exp_design, dia_params, diann_version, charge, missed_c
logger.info(f"Triqler input file is saved as {exp_out_prefix}_triqler_in.tsv")
del out_triqler

mztab_out = f"{str(Path(exp_design).stem)}_out.mzTab"
mztab_out = f"{Path(exp_design).stem}_out.mzTab"
# Convert to mzTab
diann_directory.convert_to_mztab(
report=report,
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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-thirdparty=3.0.0"
conda "bioconda::openms-thirdparty=3.1.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.0.0--h9ee0642_1' :
'biocontainers/openms-thirdparty:3.0.0--h9ee0642_1' }"
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.1.0--h9ee0642_1' :
'biocontainers/openms-thirdparty:3.1.0--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-thirdparty=3.0.0"
conda "bioconda::openms-thirdparty=3.1.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.0.0--h9ee0642_1' :
'biocontainers/openms-thirdparty:3.0.0--h9ee0642_1' }"
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.1.0--h9ee0642_1' :
'biocontainers/openms-thirdparty:3.1.0--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-thirdparty=3.0.0"
conda "bioconda::openms-thirdparty=3.1.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.0.0--h9ee0642_1' :
'biocontainers/openms-thirdparty:3.0.0--h9ee0642_1' }"
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.1.0--h9ee0642_1' :
'biocontainers/openms-thirdparty:3.1.0--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-thirdparty=3.0.0"
conda "bioconda::openms-thirdparty=3.1.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.0.0--h9ee0642_1' :
'biocontainers/openms-thirdparty:3.0.0--h9ee0642_1' }"
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.1.0--h9ee0642_1' :
'biocontainers/openms-thirdparty:3.1.0--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-thirdparty=3.0.0"
conda "bioconda::openms-thirdparty=3.1.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.0.0--h9ee0642_1' :
'biocontainers/openms-thirdparty:3.0.0--h9ee0642_1' }"
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.1.0--h9ee0642_1' :
'biocontainers/openms-thirdparty:3.1.0--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-thirdparty=3.0.0"
conda "bioconda::openms-thirdparty=3.1.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.0.0--h9ee0642_1' :
'biocontainers/openms-thirdparty:3.0.0--h9ee0642_1' }"
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.1.0--h9ee0642_1' :
'biocontainers/openms-thirdparty:3.1.0--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-thirdparty=3.0.0"
conda "bioconda::openms-thirdparty=3.1.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.0.0--h9ee0642_1' :
'biocontainers/openms-thirdparty:3.0.0--h9ee0642_1' }"
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.1.0--h9ee0642_1' :
'biocontainers/openms-thirdparty:3.1.0--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-thirdparty=3.0.0"
conda "bioconda::openms-thirdparty=3.1.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.0.0--h9ee0642_1' :
'biocontainers/openms-thirdparty:3.0.0--h9ee0642_1' }"
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.1.0--h9ee0642_1' :
'biocontainers/openms-thirdparty:3.1.0--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-thirdparty=3.0.0"
conda "bioconda::openms-thirdparty=3.1.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.0.0--h9ee0642_1' :
'biocontainers/openms-thirdparty:3.0.0--h9ee0642_1' }"
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.1.0--h9ee0642_1' :
'biocontainers/openms-thirdparty:3.1.0--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 "bioconda::openms-thirdparty=3.0.0"
conda "bioconda::openms-thirdparty=3.1.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.0.0--h9ee0642_1' :
'biocontainers/openms-thirdparty:3.0.0--h9ee0642_1' }"
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.1.0--h9ee0642_1' :
'biocontainers/openms-thirdparty:3.1.0--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-thirdparty=3.0.0"
conda "bioconda::openms-thirdparty=3.1.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.0.0--h9ee0642_1' :
'biocontainers/openms-thirdparty:3.0.0--h9ee0642_1' }"
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.1.0--h9ee0642_1' :
'biocontainers/openms-thirdparty:3.1.0--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-thirdparty=3.0.0"
conda "bioconda::openms-thirdparty=3.1.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.0.0--h9ee0642_1' :
'biocontainers/openms-thirdparty:3.0.0--h9ee0642_1' }"
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.1.0--h9ee0642_1' :
'biocontainers/openms-thirdparty:3.1.0--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-thirdparty=3.0.0"
conda "bioconda::openms-thirdparty=3.1.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.0.0--h9ee0642_1' :
'biocontainers/openms-thirdparty:3.0.0--h9ee0642_1' }"
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.1.0--h9ee0642_1' :
'biocontainers/openms-thirdparty:3.1.0--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-thirdparty=3.0.0"
conda "bioconda::openms-thirdparty=3.1.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.0.0--h9ee0642_1' :
'biocontainers/openms-thirdparty:3.0.0--h9ee0642_1' }"
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.1.0--h9ee0642_1' :
'biocontainers/openms-thirdparty:3.1.0--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-thirdparty=3.0.0"
conda "bioconda::openms-thirdparty=3.1.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.0.0--h9ee0642_1' :
'biocontainers/openms-thirdparty:3.0.0--h9ee0642_1' }"
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.1.0--h9ee0642_1' :
'biocontainers/openms-thirdparty:3.1.0--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-thirdparty=3.0.0"
conda "bioconda::openms-thirdparty=3.1.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.0.0--h9ee0642_1' :
'biocontainers/openms-thirdparty:3.0.0--h9ee0642_1' }"
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.1.0--h9ee0642_1' :
'biocontainers/openms-thirdparty:3.1.0--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-thirdparty=3.0.0"
conda "bioconda::openms-thirdparty=3.1.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.0.0--h9ee0642_1' :
'biocontainers/openms-thirdparty:3.0.0--h9ee0642_1' }"
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.1.0--h9ee0642_1' :
'biocontainers/openms-thirdparty:3.1.0--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-thirdparty=3.0.0"
conda "bioconda::openms-thirdparty=3.1.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.0.0--h9ee0642_1' :
'biocontainers/openms-thirdparty:3.0.0--h9ee0642_1' }"
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.1.0--h9ee0642_1' :
'biocontainers/openms-thirdparty:3.1.0--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-thirdparty=3.0.0"
conda "bioconda::openms-thirdparty=3.1.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.0.0--h9ee0642_1' :
'biocontainers/openms-thirdparty:3.0.0--h9ee0642_1' }"
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.1.0--h9ee0642_1' :
'biocontainers/openms-thirdparty:3.1.0--h9ee0642_1' }"

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

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

input:
tuple val(meta), path(mzml_file), path(id_file)
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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-thirdparty=3.0.0"
conda "bioconda::openms-thirdparty=3.1.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.0.0--h9ee0642_1' :
'biocontainers/openms-thirdparty:3.0.0--h9ee0642_1' }"
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.1.0--h9ee0642_1' :
'biocontainers/openms-thirdparty:3.1.0--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-thirdparty=3.0.0"
conda "bioconda::openms-thirdparty=3.1.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.0.0--h9ee0642_1' :
'biocontainers/openms-thirdparty:3.0.0--h9ee0642_1' }"
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.1.0--h9ee0642_1' :
'biocontainers/openms-thirdparty:3.1.0--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/searchenginemsgf/main.nf
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Expand Up @@ -3,10 +3,10 @@ process SEARCHENGINEMSGF {
label 'process_medium'
label 'openms'

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

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