Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

MSstats - relaxing default parameters. #437

Closed
wants to merge 4 commits into from
Closed

MSstats - relaxing default parameters. #437

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
f657b6f
MSstats relaxing thresholds
ypriverol Nov 12, 2024
230ebff
MSstats relaxing thresholds
ypriverol Nov 12, 2024
f584ec4
increase quantms utils to 0.0.12
ypriverol Nov 12, 2024
9bfbca5
fix default parameters
ypriverol Nov 12, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 2 additions & 2 deletions modules/local/preprocess_expdesign.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -8,8 +8,8 @@ process PREPROCESS_EXPDESIGN {

conda "bioconda::quantms-utils=0.0.11"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.11--pyhdfd78af_0' :
'biocontainers/quantms-utils:0.0.11--pyhdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.12--pyhdfd78af_0' :
'biocontainers/quantms-utils:0.0.12--pyhdfd78af_0' }"

input:
path design
Expand Down
4 changes: 2 additions & 2 deletions modules/local/samplesheet_check.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5,8 +5,8 @@ process SAMPLESHEET_CHECK {

conda "bioconda::quantms-utils=0.0.11"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.11--pyhdfd78af_0' :
'biocontainers/quantms-utils:0.0.11--pyhdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.12--pyhdfd78af_0' :
'biocontainers/quantms-utils:0.0.12--pyhdfd78af_0' }"

input:
path input_file
Expand Down
8 changes: 4 additions & 4 deletions nextflow.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -211,20 +211,20 @@ params {


// MSstats general options
msstats_remove_one_feat_prot = true
msstats_remove_one_feat_prot = false
ref_condition = null
contrasts = 'pairwise'
msstats_threshold = 0.05
skip_post_msstats = false

// MSstats LFQ options
msstatslfq_removeFewMeasurements = true
msstatslfq_removeFewMeasurements = false
msstatslfq_feature_subset_protein = 'top3'
msstatslfq_quant_summary_method = 'TMP'

// MSstats ISO options
msstatsiso_useunique_peptide = true
msstatsiso_rmpsm_withfewmea_withinrun = true
msstatsiso_useunique_peptide = false
msstatsiso_rmpsm_withfewmea_withinrun = false
msstatsiso_summaryformultiple_psm = 'sum'
msstatsiso_summarization_method = 'msstats'
msstatsiso_global_norm = true
Expand Down
10 changes: 5 additions & 5 deletions nextflow_schema.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -1169,25 +1169,25 @@
"type": "boolean",
"description": "Omit proteins with only one quantified feature?",
"fa_icon": "far fa-check-square",
"default": true
"default": false
},
"msstatslfq_removeFewMeasurements": {
"type": "boolean",
"description": "Keep features with only one or two measurements across runs?",
"description": "Remove features with only one or two measurements across runs?",
"fa_icon": "far fa-check-square",
"default": true
"default": false
},
"msstatsiso_useunique_peptide": {
"type": "boolean",
"description": "Use unique peptide for each protein",
"fa_icon": "far fa-check-square",
"default": true
"default": false
},
"msstatsiso_rmpsm_withfewmea_withinrun": {
"type": "boolean",
"description": "Remove the features that have 1 or 2 measurements within each run",
"fa_icon": "far fa-check-square",
"default": true
"default": false
},
"msstatsiso_summaryformultiple_psm": {
"type": "string",
Expand Down
Loading