|
| 1 | +/* |
| 2 | +======================================================================================== |
| 3 | + ID/PSM processing module options — shared across DDA workflows |
| 4 | +======================================================================================== |
| 5 | +*/ |
| 6 | + |
| 7 | +process { |
| 8 | + |
| 9 | + // FDRCONSENSUSID |
| 10 | + withName: '.*:FDR_CONSENSUSID' { |
| 11 | + ext.args = "-PSM true -protein false" |
| 12 | + } |
| 13 | + |
| 14 | + // ID_SCORE_SWITCHER for phospho scoring |
| 15 | + withName: '.*:ID:PHOSPHO_SCORING:ID_SCORE_SWITCHER' { |
| 16 | + ext.args = [ |
| 17 | + "-new_score_orientation lower_better", |
| 18 | + "-old_score \"q-value\"", |
| 19 | + "-new_score_type \"Posterior Error Probability\"", |
| 20 | + "-debug $params.idscoreswitcher_debug" |
| 21 | + ].join(' ').trim() |
| 22 | + } |
| 23 | + |
| 24 | + // ONSITE phospho scoring |
| 25 | + withName: '.*:ID:PHOSPHO_SCORING:ONSITE' { |
| 26 | + ext.args = "-debug $params.onsite_debug" |
| 27 | + } |
| 28 | + |
| 29 | + // PERCOLATOR |
| 30 | + withName: '.*:PERCOLATOR' { |
| 31 | + ext.args = [ |
| 32 | + "-debug $params.percolator_debug", |
| 33 | + (params.fdr_level != 'psm_level_fdrs') ? "-" + params.fdr_level : "" |
| 34 | + ].join(' ').trim() |
| 35 | + } |
| 36 | + |
| 37 | + // EPIFANY |
| 38 | + withName: '.*:PROTEIN_INFERENCE_EPIFANY' { |
| 39 | + ext.args = "-keep_best_psm_only false -debug $params.protein_inference_debug" |
| 40 | + } |
| 41 | + |
| 42 | + // PROTEIN_INFERENCE (generic) |
| 43 | + withName: '.*:PROTEIN_INFERENCE' { |
| 44 | + ext.args = "-debug $params.protein_inference_debug" |
| 45 | + } |
| 46 | + |
| 47 | + // PSM FDR control ID_FILTER |
| 48 | + withName: '.*:ID:PSM_FDR_CONTROL:ID_FILTER' { |
| 49 | + ext.args = "-score:psm \"$params.run_fdr_cutoff\"" |
| 50 | + ext.suffix = '.idXML' |
| 51 | + } |
| 52 | + |
| 53 | + // DDA_ID PSM FDR control ID_FILTER |
| 54 | + withName: '.*:DDA_ID:PSM_FDR_CONTROL:ID_FILTER' { |
| 55 | + ext.args = "-score:psm \"$params.run_fdr_cutoff\"" |
| 56 | + ext.suffix = '.idXML' |
| 57 | + } |
| 58 | + |
| 59 | + // MS2RESCORE |
| 60 | + withName: 'MSRESCORE_FEATURES' { |
| 61 | + ext.args = [ |
| 62 | + "--ms2_model ${params.ms2features_model}", |
| 63 | + "--calibration_set_size ${params.ms2features_calibration}", |
| 64 | + params.ms2features_generators.trim() ? "--feature_generators ${params.ms2features_generators}" : '' |
| 65 | + ].join(' ').trim() |
| 66 | + } |
| 67 | + |
| 68 | + // DDA_ID phospho scoring ID_SCORE_SWITCHER |
| 69 | + withName: '.*:DDA_ID:PHOSPHO_SCORING:ID_SCORE_SWITCHER' { |
| 70 | + ext.args = [ |
| 71 | + "-new_score_orientation lower_better", |
| 72 | + "-old_score \"q-value\"", |
| 73 | + "-new_score_type \"Posterior Error Probability\"", |
| 74 | + "-debug $params.idscoreswitcher_debug" |
| 75 | + ].join(' ').trim() |
| 76 | + } |
| 77 | +} |
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