remove unused multiqc channel which used to just plot plddt, and blocks the way for PR nf-core#450

keiran-rowell-unsw · keiran-rowell-unsw · commit 461f3bb2da8d · 2026-03-31T16:00:00.000+11:00
diff --git a/main.nf b/main.nf
@@ -67,7 +67,6 @@ workflow NFCORE_PROTEINFOLD {
 
     main:
     ch_samplesheet       = samplesheet
-    ch_multiqc           = channel.empty()
     ch_versions          = channel.empty()
     ch_report_input      = channel.empty()
     ch_top_ranked_model  = channel.empty()
@@ -136,7 +135,6 @@ workflow NFCORE_PROTEINFOLD {
             PREPARE_ALPHAFOLD2_DBS.out.pdb_seqres,
             PREPARE_ALPHAFOLD2_DBS.out.uniprot
         )
-        ch_multiqc      = ch_multiqc.mix(ALPHAFOLD2.out.multiqc_report.collect())
         ch_versions     = ch_versions.mix(ALPHAFOLD2.out.versions)
         ch_report_input = ch_report_input
                             .mix(
@@ -195,7 +193,6 @@ workflow NFCORE_PROTEINFOLD {
             PREPARE_ALPHAFOLD3_DBS.out.uniprot
         )
 
-        ch_multiqc      = ch_multiqc.mix(ALPHAFOLD3.out.multiqc_report)
         ch_versions     = ch_versions.mix(ALPHAFOLD3.out.versions)
         ch_report_input = ch_report_input
                             .mix(
@@ -240,7 +237,6 @@ workflow NFCORE_PROTEINFOLD {
             params.colabfold_num_recycles
         )
 
-        ch_multiqc          = ch_multiqc.mix(COLABFOLD.out.multiqc_report)
         ch_versions         = ch_versions.mix(COLABFOLD.out.versions)
         ch_report_input = ch_report_input
                             .mix(
@@ -279,7 +275,6 @@ workflow NFCORE_PROTEINFOLD {
             params.esmfold_num_recycles
         )
 
-        ch_multiqc      = ch_multiqc.mix(ESMFOLD.out.multiqc_report.collect())
         ch_versions     = ch_versions.mix(ESMFOLD.out.versions)
         ch_report_input = ch_report_input
                             .mix(
@@ -324,7 +319,6 @@ workflow NFCORE_PROTEINFOLD {
             PREPARE_ROSETTAFOLD_ALL_ATOM_DBS.out.pdb100,
             PREPARE_ROSETTAFOLD_ALL_ATOM_DBS.out.rfaa_paper_weights
         )
-        ch_multiqc      = ch_multiqc.mix(ROSETTAFOLD_ALL_ATOM.out.multiqc_report.collect())
         ch_versions     = ch_versions.mix(ROSETTAFOLD_ALL_ATOM.out.versions)
         ch_report_input = ch_report_input
                             .mix(
@@ -396,7 +390,6 @@ workflow NFCORE_PROTEINFOLD {
             PREPARE_HELIXFOLD3_DBS.out.helixfold3_init_models,
             PREPARE_HELIXFOLD3_DBS.out.helixfold3_maxit_src
         )
-        ch_multiqc      = ch_multiqc.mix(HELIXFOLD3.out.multiqc_report.collect())
         ch_versions     = ch_versions.mix(HELIXFOLD3.out.versions)
         ch_report_input = ch_report_input
                             .mix(
@@ -446,7 +439,6 @@ workflow NFCORE_PROTEINFOLD {
             PREPARE_ROSETTAFOLD2NA_DBS.out.rna,
             PREPARE_ROSETTAFOLD2NA_DBS.out.rosettafold2na_weights
         )
-        ch_multiqc      = ch_multiqc.mix(ROSETTAFOLD2NA.out.multiqc_report.collect())
         ch_versions     = ch_versions.mix(ROSETTAFOLD2NA.out.versions)
         ch_report_input = ch_report_input
                             .mix(
@@ -501,7 +493,6 @@ workflow NFCORE_PROTEINFOLD {
             PREPARE_COLABFOLD_DBS_BOLTZ.out.uniref30,
             params.use_msa_server
         )
-        ch_multiqc      = ch_multiqc.mix(BOLTZ.out.multiqc_report)
         ch_versions     = ch_versions.mix(BOLTZ.out.versions)
         ch_report_input = ch_report_input
                             .mix(
@@ -531,7 +522,6 @@ workflow NFCORE_PROTEINFOLD {
         params.skip_multiqc,
         params.outdir,
         ch_versions,
-        ch_multiqc,
         ch_multiqc_config,
         ch_multiqc_custom_config,
         ch_multiqc_logo,
@@ -540,7 +530,7 @@ workflow NFCORE_PROTEINFOLD {
     )
 
     emit:
-    multiqc_report = ch_multiqc
+    multiqc_report = POST_PROCESSING.out.multiqc_report
 }
 
 /*
diff --git a/modules/local/colabfold_batch/main.nf b/modules/local/colabfold_batch/main.nf
@@ -18,7 +18,7 @@ process COLABFOLD_BATCH {
     tuple val(meta), path ("${meta.id}_colabfold.pdb")      , emit: top_ranked_pdb
     tuple val(meta), path ("raw/*relaxed_rank_*.pdb")       , emit: pdb
     tuple val(meta), path ("${meta.id}_colabfold_msa.tsv")  , emit: msa
-    tuple val(meta), path ("${meta.id}_plddt.tsv")          , emit: multiqc
+    tuple val(meta), path ("${meta.id}_plddt.tsv")          , emit: plddt
     tuple val(meta), path ("${meta.id}_*_pae.tsv")          , optional: true, emit: paes
     tuple val(meta), path ("${meta.id}_0_pae.tsv")          , optional: true, emit: pae
     tuple val(meta), path ("${meta.id}_ptm.tsv")            , optional: true, emit: ptms
diff --git a/modules/local/run_alphafold2/main.nf b/modules/local/run_alphafold2/main.nf
@@ -29,7 +29,7 @@ process RUN_ALPHAFOLD2 {
     path ("raw/**")                                         , emit: raw
     tuple val(meta), path ("${meta.id}_alphafold2.pdb")     , emit: top_ranked_pdb
     tuple val(meta), path ("raw/ranked*.pdb")               , emit: pdb
-    tuple val(meta), path ("${meta.id}_plddt.tsv")          , emit: multiqc
+    tuple val(meta), path ("${meta.id}_plddt.tsv")          , emit: plddt
     tuple val(meta), path ("${meta.id}_alphafold2_msa.tsv") , emit: msa
     // Note: alphafold2_model_preset == "monomer" the pae file won't exist, thus the optional
     tuple val(meta), path ("${meta.id}_*_pae.tsv")          , optional: true, emit: paes
diff --git a/modules/local/run_alphafold2_pred/main.nf b/modules/local/run_alphafold2_pred/main.nf
@@ -28,7 +28,7 @@ process RUN_ALPHAFOLD2_PRED {
     tuple val(meta), path ("${meta.id}_alphafold2.pdb")     , emit: top_ranked_pdb
     tuple val(meta), path ("raw/ranked*.pdb")               , emit: pdb
     tuple val(meta), path ("${meta.id}_alphafold2_msa.tsv") , emit: msa
-    tuple val(meta), path ("${meta.id}_plddt.tsv")          , emit: multiqc
+    tuple val(meta), path ("${meta.id}_plddt.tsv")          , emit: plddt
     //Note: alphafold2_model_preset == "monomer" the pae file won't exist.
     tuple val(meta), path ("${meta.id}_*_pae.tsv")          , optional: true, emit: paes
     tuple val(meta), path ("${meta.id}_0_pae.tsv")          , optional: true, emit: pae
diff --git a/modules/local/run_alphafold3/main.nf b/modules/local/run_alphafold3/main.nf
@@ -21,7 +21,7 @@ process RUN_ALPHAFOLD3 {
     path ("raw/**")                                         , emit: raw
     tuple val(meta), path ("${meta.id}_alphafold3.cif")     , emit: top_ranked_cif
     tuple val(meta), path ("raw/*ranked_*.cif")             , emit: cif
-    tuple val(meta), path ("${meta.id}_plddt.tsv")          , emit: multiqc
+    tuple val(meta), path ("${meta.id}_plddt.tsv")          , emit: plddt
     tuple val(meta), path ("${meta.id}_alphafold3_msa.tsv") , emit: msa
     tuple val(meta), path ("${meta.id}_0_pae.tsv")          , emit: pae
     tuple val(meta), path ("${meta.id}_ptm.tsv")            , emit: ptms
diff --git a/modules/local/run_boltz/main.nf b/modules/local/run_boltz/main.nf
@@ -21,7 +21,7 @@ process RUN_BOLTZ {
     tuple val(meta), path ("boltz_results_*/processed/msa/*.npz")               , emit: msa
     tuple val(meta), path ("boltz_results_*/processed/structures/*.npz")        , emit: structures
     tuple val(meta), path ("boltz_results_*/predictions/*/confidence*.json")    , emit: confidence
-    tuple val(meta), path ("${meta.id}_plddt.tsv")                              , emit: multiqc
+    tuple val(meta), path ("${meta.id}_plddt.tsv")                              , emit: plddt
     tuple val(meta), path ("${meta.id}_boltz.pdb")                              , emit: top_ranked_pdb
     tuple val(meta), path ("boltz_results_*/predictions/*/*.pdb")               , emit: pdb
     tuple val(meta), path ("boltz_results_*/predictions/*/plddt_*model_0.npz")  , emit: plddt
diff --git a/modules/local/run_esmfold/main.nf b/modules/local/run_esmfold/main.nf
@@ -13,7 +13,7 @@ process RUN_ESMFOLD {
     output:
     tuple val(meta), path ("${meta.id}_esmfold.pdb")  , emit: top_ranked_pdb
     tuple val(meta), path ("*.pdb")                   , emit: pdb
-    tuple val(meta), path ("${meta.id}_plddt.tsv")    , emit: multiqc
+    tuple val(meta), path ("${meta.id}_plddt.tsv")    , emit: plddt
     path "versions.yml"                               , emit: versions
 
     when:
diff --git a/modules/local/run_helixfold3/main.nf b/modules/local/run_helixfold3/main.nf
@@ -30,7 +30,7 @@ process RUN_HELIXFOLD3 {
     tuple val(meta), path ("${meta.id}_helixfold3.pdb")     , emit: top_ranked_pdb
     tuple val(meta), path ("${meta.id}_helixfold3.cif")     , emit: main_cif
     tuple val(meta), path ("raw/ranked*.pdb")    , emit: pdb
-    tuple val(meta), path ("${meta.id}_plddt.tsv")          , emit: multiqc
+    tuple val(meta), path ("${meta.id}_plddt.tsv")          , emit: plddt
     tuple val(meta), path ("${meta.id}_helixfold3_msa.tsv") , emit: msa
     // If ${meta.id}-rank*/all_results.json" doesn't have PAE vales in the key, this will be empty
     tuple val(meta), path ("${meta.id}_1_pae.tsv")          , emit: pae
diff --git a/modules/local/run_rosettafold2na/main.nf b/modules/local/run_rosettafold2na/main.nf
@@ -20,7 +20,7 @@ process RUN_ROSETTAFOLD2NA {
     path ("raw/**")                                            , emit: raw
     tuple val(meta), path("${meta.id}_rosettafold2na.pdb")     , emit: top_ranked_pdb
     tuple val(meta), path("raw/*.pdb")                         , emit: pdb
-    tuple val(meta), path("${meta.id}_plddt.tsv")              , emit: multiqc
+    tuple val(meta), path("${meta.id}_plddt.tsv")              , emit: plddt
     tuple val(meta), path("${meta.id}_rosettafold2na_msa.tsv") , emit: msa
     tuple val(meta), path("${meta.id}_0_pae.tsv")              , emit: pae
     path "versions.yml"                                        , emit: versions
diff --git a/modules/local/run_rosettafold_all_atom/main.nf b/modules/local/run_rosettafold_all_atom/main.nf
@@ -20,7 +20,7 @@ process RUN_ROSETTAFOLD_ALL_ATOM {
     output:
     path ("raw/**")                                                     , emit: raw
     tuple val(meta), path ("${meta.id}_rosettafold_all_atom.pdb")       , emit: pdb
-    tuple val(meta), path ("${meta.id}_plddt.tsv")                      , emit: multiqc
+    tuple val(meta), path ("${meta.id}_plddt.tsv")                      , emit: plddt
     tuple val(meta), path ("${meta.id}_rosettafold_all_atom_msa.tsv")   , emit: msa
     // I think there should always be PAE from the .pt PyTorch model. extract_metrics.py has condition import torch to handle this
     tuple val(meta), path ("${meta.id}_*_pae.tsv")                      , emit: paes
diff --git a/subworkflows/local/post_processing.nf b/subworkflows/local/post_processing.nf
@@ -29,7 +29,6 @@ workflow POST_PROCESSING {
     skip_multiqc
     outdir
     ch_versions
-    ch_multiqc_rep
     ch_multiqc_config
     ch_multiqc_custom_config
     ch_multiqc_logo
@@ -122,13 +121,7 @@ workflow POST_PROCESSING {
             .mix(ch_collated_versions)
 
         MULTIQC (
-            ch_multiqc_rep
-                .combine(
-                    ch_multiqc_files
-                        .collect()
-                        .map { [it] }
-                )
-                .map { meta, report_files, multiqc_files -> [ meta, report_files + multiqc_files ] },
+            ch_multiqc_files.collect().map { [[id: "proteinfold", model: "proteinfold"], it] },
             ch_multiqc_config,
             ch_multiqc_custom_config.toList(),
             ch_multiqc_logo.toList(),
diff --git a/workflows/alphafold2.nf b/workflows/alphafold2.nf
@@ -49,7 +49,6 @@ workflow ALPHAFOLD2 {
     ch_top_ranked_pdb = channel.empty()
     ch_msa            = channel.empty()
     ch_pae            = channel.empty()
-    ch_multiqc_report = channel.empty()
 
     if (alphafold2_model_preset != 'multimer') {
         ch_samplesheet
@@ -83,16 +82,6 @@ workflow ALPHAFOLD2 {
             ch_uniprot
         )
 
-        RUN_ALPHAFOLD2
-            .out
-            .multiqc
-            .map { it -> it[1] }
-            .toSortedList()
-            .map { it ->
-                [ [ "model": "alphafold2" ], it.flatten() ]
-            }
-            .set { ch_multiqc_report }
-
         ch_pdb            = ch_pdb.mix(RUN_ALPHAFOLD2.out.pdb)
         ch_top_ranked_pdb = ch_top_ranked_pdb.mix(RUN_ALPHAFOLD2.out.top_ranked_pdb)
         ch_msa            = ch_msa.mix(RUN_ALPHAFOLD2.out.msa)
@@ -143,16 +132,6 @@ workflow ALPHAFOLD2 {
             ch_uniprot
         )
 
-        RUN_ALPHAFOLD2_PRED
-            .out
-            .multiqc
-            .map { it -> it[1] }
-            .toSortedList()
-            .map { it ->
-                [ [ "model": "alphafold2" ], it.flatten() ]
-            }
-            .set { ch_multiqc_report }
-
         ch_top_ranked_pdb = ch_top_ranked_pdb.mix(RUN_ALPHAFOLD2_PRED.out.top_ranked_pdb)
         ch_pdb            = ch_pdb.mix(RUN_ALPHAFOLD2_PRED.out.pdb)
         ch_msa            = ch_msa.mix(RUN_ALPHAFOLD2_PRED.out.msa)
@@ -197,7 +176,6 @@ workflow ALPHAFOLD2 {
     pdb            = ch_pdb_final            // channel: [ meta, /path/to/*.pdb ]
     msa            = ch_msa_final            // channel: [ meta, /path/to/*.pdb, /path/to/*_coverage.png ]  // Would prefer channel: [ meta, /path/to/*_msa.tsv ]
     pae            = ch_pae_final            // channel: [ meta, /path/to/*_0_pae.tsv]
-    multiqc_report = ch_multiqc_report       // channel: /path/to/multiqc_report.html
     versions       = ch_versions             // channel: [ path(versions.yml) ]
 }
 
diff --git a/workflows/alphafold3.nf b/workflows/alphafold3.nf
@@ -41,7 +41,6 @@ workflow ALPHAFOLD3 {
     ch_pdb_final      = channel.empty()
     ch_top_ranked_pdb = channel.empty()
     ch_msa_final      = channel.empty()
-    ch_multiqc_report = channel.empty()
 
     FASTA_TO_ALPHAFOLD3_JSON(ch_samplesheet)
     ch_versions       = ch_versions.mix(FASTA_TO_ALPHAFOLD3_JSON.out.versions)
@@ -124,17 +123,6 @@ workflow ALPHAFOLD3 {
         }
         .set { ch_msa_final }
 
-    // Prepare report input
-    RUN_ALPHAFOLD3
-        .out
-        .multiqc
-        .map { it -> it[1] }
-        .toSortedList()
-        .map { it ->
-            [ [ "model": "alphafold3" ], it.flatten() ]
-        }
-        .set { ch_multiqc_report }
-
     // Prepare dummy pae input
     RUN_ALPHAFOLD3
         .out
@@ -151,7 +139,6 @@ workflow ALPHAFOLD3 {
     pdb            = ch_pdb_final      // channel: [ meta, /path/to/*.pdb, ...,/path/to/*.pdb ]
     msa            = ch_msa_final      // channel: [ meta, /path/to/*.pdb, /path/to/*_coverage.png ]
     pae            = ch_pae_final      // channel: [ meta, path/to/*_pae.tsv ]
-    multiqc_report = ch_multiqc_report // channel: /path/to/multiqc_report.html
     versions       = ch_versions       // channel: [ path(versions.yml) ]
 }
 
diff --git a/workflows/boltz.nf b/workflows/boltz.nf
@@ -175,22 +175,13 @@ workflow BOLTZ {
         }
         .set { ch_pae }
 
-    RUN_BOLTZ
-        .out
-        .multiqc
-        .map { it -> it[1] }
-        .collect(sort: true)
-        .map { it ->  [ [ "model": "boltz"], it.flatten() ] }
-        .set { ch_multiqc_report  }
-
     ch_versions       = ch_versions.mix(RUN_BOLTZ.out.versions)
 
     emit:
     versions        = ch_versions
     msa             = ch_msa
     structures      = RUN_BOLTZ.out.structures
     confidence      = RUN_BOLTZ.out.confidence
-    multiqc_report  = ch_multiqc_report
     top_ranked_pdb  = ch_top_ranked_pdb
     pdb             = ch_pdb
     pae             = ch_pae
diff --git a/workflows/colabfold.nf b/workflows/colabfold.nf
@@ -37,7 +37,6 @@ workflow COLABFOLD {
     num_recycles           // int: Number of recycles for colabfold
 
     main:
-    ch_multiqc_report = channel.empty()
 
     if (params.use_msa_server) {
         //
@@ -113,22 +112,11 @@ workflow COLABFOLD {
     modeChannel(COLABFOLD_BATCH.out.msa, "colabfold").set { ch_msa_final }
     modeChannel(COLABFOLD_BATCH.out.pae, "colabfold").set { ch_pae_final }
 
-    COLABFOLD_BATCH
-        .out
-        .multiqc
-        .map { it -> it[1] }
-        .toSortedList()
-        .map { it ->
-            [ [ "model":"colabfold"], it.flatten() ]
-        }
-        .set { ch_multiqc_report  }
-
     emit:
     top_ranked_pdb = ch_top_ranked_pdb // channel: [ meta, /path/to/*.pdb ]
     pdb            = ch_pdb_final      // channel: [ id, /path/to/*.pdb ]
     msa            = ch_msa_final      // channel: [ meta, /path/to/*.pdb, /path/to/*_coverage.png ]
     pae            = ch_pae_final      // channel: [ id, /path/to/*_pae.tsv ]
-    multiqc_report = ch_multiqc_report // channel: /path/to/multiqc_report.html
     versions       = ch_versions       // channel: [ path(versions.yml) ]
 }
 
diff --git a/workflows/esmfold.nf b/workflows/esmfold.nf
@@ -56,21 +56,10 @@ workflow ESMFOLD {
         ch_versions = ch_versions.mix(RUN_ESMFOLD.out.versions)
     }
 
-    RUN_ESMFOLD
-        .out
-        .multiqc
-        .map { it -> it[1] }
-        .toSortedList()
-        .map { it ->
-            [ [ "model": "esmfold"], it.flatten() ]
-        }
-        .set { ch_multiqc_report  }
-
     modeChannel(RUN_ESMFOLD.out.pdb, "esmfold").set { ch_pdb_final }
 
     emit:
     pdb            = ch_pdb_final      // channel: [ id, /path/to/*.pdb ]
-    multiqc_report = ch_multiqc_report // channel: /path/to/multiqc_report.html
     versions       = ch_versions       // channel: [ path(versions.yml) ]
 }
 
diff --git a/workflows/helixfold3.nf b/workflows/helixfold3.nf
@@ -47,7 +47,6 @@ workflow HELIXFOLD3 {
     main:
     ch_pdb            = channel.empty()
     ch_top_ranked_pdb = channel.empty()
-    ch_multiqc_report = channel.empty()
 
     //
     // SUBWORKFLOW: Run helixfold3
@@ -77,16 +76,6 @@ workflow HELIXFOLD3 {
         ch_helixfold3_maxit_src
     )
 
-    RUN_HELIXFOLD3
-        .out
-        .multiqc
-        .map { it ->  it[1] }
-        .toSortedList()
-        .map { it ->
-            [ [ "model": "helixfold3" ], it.flatten() ]
-        }
-        .set { ch_multiqc_report }
-
     ch_pdb      = ch_pdb.mix(RUN_HELIXFOLD3.out.pdb)
     ch_versions = ch_versions.mix(RUN_HELIXFOLD3.out.versions)
 
@@ -119,7 +108,6 @@ workflow HELIXFOLD3 {
     pdb            = ch_pdb_final      // channel: [ id, /path/to/*.pdb ]
     msa            = ch_msa_final      // channel: [ id, /path/to/*_msa.tsv ]
     pae            = ch_pae_final      // channel: [ id, /path/to/*_pae.tsv ]
-    multiqc_report = ch_multiqc_report // channel: /path/to/multiqc_report.html
     versions       = ch_versions       // channel: [ path(versions.yml) ]
 }
 
diff --git a/workflows/rosettafold2na.nf b/workflows/rosettafold2na.nf
diff --git a/workflows/rosettafold_all_atom.nf b/workflows/rosettafold_all_atom.nf
