From 1c414bb6dae2ed3ee2ec27ed8cf726061579312f Mon Sep 17 00:00:00 2001 From: Julianus Pfeuffer Date: Mon, 28 Mar 2022 16:03:26 +0200 Subject: [PATCH 1/4] Use IDs before consensusID for pmultiqc --- main.nf | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/main.nf b/main.nf index 9b038db..64b8e11 100644 --- a/main.nf +++ b/main.nf @@ -775,7 +775,7 @@ process percolator { tuple mzml_id, file(id_file) from id_files_idx_feat output: - tuple mzml_id, file("${id_file.baseName}_perc.idXML"), val("MS:1001491") into (id_files_perc, id_files_perc_consID) + tuple mzml_id, file("${id_file.baseName}_perc.idXML"), val("MS:1001491") into (id_files_perc, id_files_perc_consID, id_files_perc_multiqc) file "*.log" when: @@ -854,7 +854,7 @@ process idpep { tuple mzml_id, file(id_file) from id_files_idx_ForIDPEP_FDR.mix(id_files_idx_ForIDPEP_noFDR) output: - tuple mzml_id, file("${id_file.baseName}_idpep.idXML"), val("q-value_score") into (id_files_idpep, id_files_idpep_consID) + tuple mzml_id, file("${id_file.baseName}_idpep.idXML"), val("q-value_score") into (id_files_idpep, id_files_idpep_consID, id_files_idpep_pmultiqc) file "*.log" when: @@ -1226,8 +1226,8 @@ process pmultiqc { input: file design from ch_expdesign_multiqc file 'mzMLs/*' from ch_plfq.multiqc_mzmls.collect() - file 'proteomicslfq/*' from ch_out_mzTab_multiqc.merge(ch_out_consensusXML_multiqc).merge(ch_out_msstats_multiqc) - file 'raw_ids/*' from ch_plfq.multiqc_ids.collect() + file 'proteomicslfq/*' from ch_out_mzTab_multiqc.merge(ch_out_consensusXML_multiqc).merge(ch_out_msstats_multiqc) + file 'raw_ids/*' from id_files_idpep_consID.mix(id_files_perc_consID) output: file '*.html' into ch_multiqc_report From d89c726889866ff8632fa80bb395bb0184228738 Mon Sep 17 00:00:00 2001 From: Julianus Pfeuffer Date: Mon, 28 Mar 2022 16:28:54 +0200 Subject: [PATCH 2/4] Update main.nf --- main.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/main.nf b/main.nf index 64b8e11..fff07aa 100644 --- a/main.nf +++ b/main.nf @@ -854,7 +854,7 @@ process idpep { tuple mzml_id, file(id_file) from id_files_idx_ForIDPEP_FDR.mix(id_files_idx_ForIDPEP_noFDR) output: - tuple mzml_id, file("${id_file.baseName}_idpep.idXML"), val("q-value_score") into (id_files_idpep, id_files_idpep_consID, id_files_idpep_pmultiqc) + tuple mzml_id, file("${id_file.baseName}_idpep.idXML"), val("q-value_score") into (id_files_idpep, id_files_idpep_consID, id_files_idpep_multiqc) file "*.log" when: @@ -1227,7 +1227,7 @@ process pmultiqc { file design from ch_expdesign_multiqc file 'mzMLs/*' from ch_plfq.multiqc_mzmls.collect() file 'proteomicslfq/*' from ch_out_mzTab_multiqc.merge(ch_out_consensusXML_multiqc).merge(ch_out_msstats_multiqc) - file 'raw_ids/*' from id_files_idpep_consID.mix(id_files_perc_consID) + file 'raw_ids/*' from id_files_idpep_multiqc.mix(id_files_perc_multiqc) output: file '*.html' into ch_multiqc_report From c6436da099ca2fdef936c51134901537dacb132c Mon Sep 17 00:00:00 2001 From: Julianus Pfeuffer Date: Tue, 29 Mar 2022 11:03:09 +0200 Subject: [PATCH 3/4] debug --- main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/main.nf b/main.nf index fff07aa..719e63d 100644 --- a/main.nf +++ b/main.nf @@ -1227,7 +1227,7 @@ process pmultiqc { file design from ch_expdesign_multiqc file 'mzMLs/*' from ch_plfq.multiqc_mzmls.collect() file 'proteomicslfq/*' from ch_out_mzTab_multiqc.merge(ch_out_consensusXML_multiqc).merge(ch_out_msstats_multiqc) - file 'raw_ids/*' from id_files_idpep_multiqc.mix(id_files_perc_multiqc) + file 'raw_ids/*' from id_files_idpep_multiqc.mix(id_files_perc_multiqc).view() output: file '*.html' into ch_multiqc_report From abe0388f793911107616c7d632c14a1b2f3423f8 Mon Sep 17 00:00:00 2001 From: Julianus Pfeuffer Date: Tue, 29 Mar 2022 11:14:15 +0200 Subject: [PATCH 4/4] Update main.nf --- main.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/main.nf b/main.nf index 719e63d..968e92e 100644 --- a/main.nf +++ b/main.nf @@ -1227,11 +1227,11 @@ process pmultiqc { file design from ch_expdesign_multiqc file 'mzMLs/*' from ch_plfq.multiqc_mzmls.collect() file 'proteomicslfq/*' from ch_out_mzTab_multiqc.merge(ch_out_consensusXML_multiqc).merge(ch_out_msstats_multiqc) - file 'raw_ids/*' from id_files_idpep_multiqc.mix(id_files_perc_multiqc).view() + file 'raw_ids/*' from id_files_idpep_multiqc.mix(id_files_perc_multiqc)[1].view() output: file '*.html' into ch_multiqc_report - file '*.db' + file '*.db' script: """