diff --git a/CHANGELOG.md b/CHANGELOG.md
index 25051396..bdb35127 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -12,6 +12,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[#179](https://github.com/nf-core/proteinfold/issues/179)]- Produce an interactive html report for the predicted structures.
 - [[#180](https://github.com/nf-core/proteinfold/issues/180)]- Implement Fooldseek.
 - [[#188](https://github.com/nf-core/proteinfold/issues/188)]- Fix colabfold image to run in gpus.
+- [[PR ##205](https://github.com/nf-core/proteinfold/pull/205)] - Change input schema from `sequence,fasta` to `id,fasta`.
+- [[PR #210](https://github.com/nf-core/proteinfold/pull/210)]- Moving post-processing logic to a subworkflow, change wave images pointing to oras to point to https and refactor module to match nf-core folder structure.
 
 ## [[1.1.1](https://github.com/nf-core/proteinfold/releases/tag/1.1.1)] - 2025-07-30
 
@@ -72,7 +74,6 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [[PR ##163](https://github.com/nf-core/proteinfold/pull/163)] - Fix full test CI.
 - [[#150]](https://github.com/nf-core/proteinfold/issues/150)] - Add thanks to the AWS Open Data Sponsorship program in `README.md`.
 - [[PR ##166](https://github.com/nf-core/proteinfold/pull/166)] - Create 2 different parameters for Colabfold and ESMfold number of recycles.
-- [[PR ##205](https://github.com/nf-core/proteinfold/pull/205)] - Change input schema from `sequence,fasta` to `id,fasta`.
 
 ### Parameters
 
diff --git a/assets/proteinfold_template.html b/assets/report_template.html
similarity index 100%
rename from assets/proteinfold_template.html
rename to assets/report_template.html
diff --git a/main.nf b/main.nf
index edb73940..d1ec1a6b 100644
--- a/main.nf
+++ b/main.nf
@@ -52,6 +52,9 @@ params.colabfold_alphafold2_params_path = getColabfoldAlphafold2ParamsPath()
 //
 // WORKFLOW: Run main analysis pipeline
 //
+
+ch_dummy_file = Channel.fromPath("$projectDir/assets/NO_FILE")
+
 workflow NFCORE_PROTEINFOLD {
 
     take:
@@ -59,14 +62,16 @@ workflow NFCORE_PROTEINFOLD {
 
     main:
     ch_samplesheet              = samplesheet
+    ch_alphafold_top_ranked_pdb = Channel.empty()
+    ch_colabfold_top_ranked_pdb = Channel.empty()
+    ch_esmfold_top_ranked_pdb   = Channel.empty()
     ch_multiqc                  = Channel.empty()
     ch_versions                 = Channel.empty()
     ch_report_input             = Channel.empty()
     ch_foldseek_db              = Channel.empty()
-    ch_colabfold_out            = Channel.empty()
-    ch_esmfold_out              = Channel.empty()
-    ch_alphafold2_out           = Channel.empty()
     requested_modes             = params.mode.toLowerCase().split(",")
+    requested_modes_size        = requested_modes.size()
+
     //
     // WORKFLOW: Run alphafold2
     //
@@ -122,16 +127,10 @@ 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(
-            ALPHAFOLD2.out.pdb.join(ALPHAFOLD2.out.msa).map{it[0]["model"] = "alphafold2"; it}
-        )
-        ALPHAFOLD2
-            .out
-            .main_pdb
-            .map{[it[0]["id"], it[0], it[1]]}
-            .set{ch_alphafold2_out}
+        ch_alphafold_top_ranked_pdb = ALPHAFOLD2.out.top_ranked_pdb
+        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(ALPHAFOLD2.out.pdb_msa)
     }
 
     //
@@ -166,23 +165,11 @@ workflow NFCORE_PROTEINFOLD {
             PREPARE_COLABFOLD_DBS.out.uniref30,
             params.num_recycles_colabfold
         )
-        ch_multiqc  = ch_multiqc.mix(COLABFOLD.out.multiqc_report)
-        ch_versions = ch_versions.mix(COLABFOLD.out.versions)
-        ch_report_input = ch_report_input.mix(
-            COLABFOLD
-                .out
-                .pdb
-                .join(COLABFOLD.out.msa)
-                .map { it[0]["model"] = "colabfold"; it }
-        )
-        COLABFOLD
-                .out
-                .main_pdb
-                .map{[it[0]["id"], it[0], it[1]]}
-                .join(COLABFOLD.out.msa
-                        .map{[it[0]["id"], it[1]]},
-                    remainder:true
-                ).set{ch_colabfold_out}
+
+        ch_colabfold_top_ranked_pdb = COLABFOLD.out.top_ranked_pdb
+        ch_multiqc                  = ch_multiqc.mix(COLABFOLD.out.multiqc_report)
+        ch_versions                 = ch_versions.mix(COLABFOLD.out.versions)
+        ch_report_input             = ch_report_input.mix(COLABFOLD.out.pdb_msa)
     }
 
     //
@@ -208,49 +195,59 @@ workflow NFCORE_PROTEINFOLD {
             ch_samplesheet,
             ch_versions,
             PREPARE_ESMFOLD_DBS.out.params,
-            params.num_recycles_esmfold
+            params.num_recycles_esmfold,
+            ch_dummy_file
         )
-        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(
-            ESMFOLD.out.pdb.combine(Channel.fromPath("$projectDir/assets/NO_FILE")).map{it[0]["model"] = "esmfold"; it}
-        )
-        ch_report_input.filter{it[0]["model"] == "esmfold"}
-            .map{[it[0]["id"], it[0], it[1], it[2]]}
-            .set{ch_esmfold_out}
+
+        ch_esmfold_top_ranked_pdb = ESMFOLD.out.top_ranked_pdb
+        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(ESMFOLD.out.pdb_msa)
     }
+
     //
-    // POST PROCESSING: generate visulaisation reports
+    // POST PROCESSING: generate visualisation reports
     //
+    // TODO: we need to validate the rest of foldseek parameters if foldseek is set to run
+    // TODO: maybe create a parameter that is run_foldseek or skip_foldsee instead as there are no more mode than can be use now
+
+    // TODO move it to pdb.config? asign as in prepare dbs
     if (params.foldseek_search == "easysearch"){
-        ch_foldseek_db = channel.value([["id": params.foldseek_db],
-                                        file(params.foldseek_db_path,
-                                            checkIfExists: true)])
+        ch_foldseek_db = channel.value([
+            [
+                id: params.foldseek_db,
+            ],
+            file(params.foldseek_db_path, checkIfExists: true)
+        ])
     }
 
-    ch_multiqc_config = params.multiqc_config ? Channel.fromPath( params.multiqc_config ) : Channel.empty()
-    ch_multiqc_logo = params.multiqc_logo   ? Channel.fromPath( params.multiqc_logo )   : Channel.empty()
+    ch_multiqc_config        = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true).first()
+    ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath( params.multiqc_config ).first()  : Channel.empty()
+    ch_multiqc_logo          = params.multiqc_logo   ? Channel.fromPath( params.multiqc_logo ).first()    : Channel.empty()
     ch_multiqc_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
-//ch_multiqc.view()
+    ch_report_template     = Channel.value(file("$projectDir/assets/report_template.html", checkIfExists: true))
+    ch_comparison_template = Channel.value(file("$projectDir/assets/comparison_template.html", checkIfExists: true))
+
     POST_PROCESSING(
         params.skip_visualisation,
-        requested_modes.size(),
+        params.mode,
+        requested_modes_size,
         ch_report_input,
-        Channel.fromPath("$projectDir/assets/proteinfold_template.html", checkIfExists: true).first(),
-        Channel.fromPath("$projectDir/assets/comparison_template.html", checkIfExists: true).first(),
+        ch_report_template,
+        ch_comparison_template,
         params.foldseek_search,
         ch_foldseek_db,
         params.skip_multiqc,
         params.outdir,
         ch_versions,
         ch_multiqc,
-        Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true).first(),
-        ch_multiqc_config.first(),
-        ch_multiqc_logo.first(),
-        ch_multiqc_methods_description.first(),
-        ch_alphafold2_out,
-        ch_esmfold_out,
-        ch_colabfold_out
+        ch_multiqc_config,
+        ch_multiqc_custom_config,
+        ch_multiqc_logo,
+        ch_multiqc_methods_description,
+        ch_alphafold_top_ranked_pdb,
+        ch_colabfold_top_ranked_pdb,
+        ch_esmfold_top_ranked_pdb
     )
 
     emit:
diff --git a/modules/local/colabfold_batch.nf b/modules/local/colabfold_batch/main.nf
similarity index 85%
rename from modules/local/colabfold_batch.nf
rename to modules/local/colabfold_batch/main.nf
index 8710f9eb..4a54dde1 100644
--- a/modules/local/colabfold_batch.nf
+++ b/modules/local/colabfold_batch/main.nf
@@ -18,11 +18,11 @@ process COLABFOLD_BATCH {
     val   numRec
 
     output:
-    tuple val(meta), path ("${meta.id}_colabfold.pdb"), emit: main_pdb
-    tuple val(meta), path ("*_relaxed_rank_*.pdb"), emit: pdb
-    tuple val(meta), path ("*_coverage.png")      , emit: msa
-    tuple val(meta), path ("*_mqc.png")           , emit: multiqc
-    path "versions.yml"                           , emit: versions
+    tuple val(meta), path ("${meta.id}_colabfold.pdb"), emit: top_ranked_pdb
+    tuple val(meta), path ("*_relaxed_rank_*.pdb")    , emit: pdb
+    tuple val(meta), path ("*_coverage.png")          , emit: msa
+    tuple val(meta), path ("*_mqc.png")               , emit: multiqc
+    path "versions.yml"                               , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
diff --git a/modules/local/combine_uniprot/environment.yml b/modules/local/combine_uniprot/environment.yml
new file mode 100644
index 00000000..a5702139
--- /dev/null
+++ b/modules/local/combine_uniprot/environment.yml
@@ -0,0 +1,8 @@
+name: combine_uniprot
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - conda-forge::grep=3.11
+  - conda-forge::sed=4.8
+  - conda-forge::tar=1.34
diff --git a/modules/local/combine_uniprot.nf b/modules/local/combine_uniprot/main.nf
similarity index 96%
rename from modules/local/combine_uniprot.nf
rename to modules/local/combine_uniprot/main.nf
index 7f4637b3..e295476d 100644
--- a/modules/local/combine_uniprot.nf
+++ b/modules/local/combine_uniprot/main.nf
@@ -1,7 +1,7 @@
 process COMBINE_UNIPROT {
     label 'process_single'
 
-    conda "conda-forge::sed=4.7"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
         'nf-core/ubuntu:20.04' }"
diff --git a/modules/local/compare_structures/environment.yml b/modules/local/compare_structures/environment.yml
new file mode 100644
index 00000000..9f657a6f
--- /dev/null
+++ b/modules/local/compare_structures/environment.yml
@@ -0,0 +1,9 @@
+name: compare_structures
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - conda-forge::biopython=1.84
+  - conda-forge::matplotlib=3.9.2
+  - conda-forge::pip=24.2
+  - conda-forge::plotly=5.24.1
diff --git a/modules/local/compare_structures.nf b/modules/local/compare_structures/main.nf
similarity index 80%
rename from modules/local/compare_structures.nf
rename to modules/local/compare_structures/main.nf
index 756d2525..f2b1b590 100644
--- a/modules/local/compare_structures.nf
+++ b/modules/local/compare_structures/main.nf
@@ -2,10 +2,10 @@ process COMPARE_STRUCTURES {
     tag   "$meta.id"
     label 'process_single'
 
-    conda "bioconda::multiqc:1.21"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/pip_biopython_matplotlib_plotly:e865101a15ad0014' :
-        'community.wave.seqera.io/library/pip_biopython_matplotlib_plotly:4d51afeb4bb75495' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/24/241f0746484727a3633f544c3747bfb77932e1c8c252e769640bd163232d9112/data' :
+        'community.wave.seqera.io/library/biopython_matplotlib_pip_plotly:35975fa0fc54b2d3' }"
 
     input:
     tuple val(meta), path(pdb)
diff --git a/modules/local/download_pdbmmcif/environment.yml b/modules/local/download_pdbmmcif/environment.yml
new file mode 100644
index 00000000..4a53be04
--- /dev/null
+++ b/modules/local/download_pdbmmcif/environment.yml
@@ -0,0 +1,7 @@
+name: download_pdbmmcif
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - conda-forge::aria2=1.36.0
+  - conda-forge::rsync=3.3.0
diff --git a/modules/local/download_pdbmmcif.nf b/modules/local/download_pdbmmcif/main.nf
similarity index 84%
rename from modules/local/download_pdbmmcif.nf
rename to modules/local/download_pdbmmcif/main.nf
index 98ef831e..a8a12963 100644
--- a/modules/local/download_pdbmmcif.nf
+++ b/modules/local/download_pdbmmcif/main.nf
@@ -6,10 +6,10 @@ process DOWNLOAD_PDBMMCIF {
     label 'process_low'
     label 'error_retry'
 
-    conda "bioconda::aria2=1.36.0 conda-forge::rsync=3.2.7"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-4a7c46784ad871c48746744c6b8dbc5d0a97b9ca:33e61a87922824f8afcecf88a7717a2d4cb514e9-0' :
-        'biocontainers/mulled-v2-4a7c46784ad871c48746744c6b8dbc5d0a97b9ca:33e61a87922824f8afcecf88a7717a2d4cb514e9-0' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/3c/3c2e1079a0721851248bd2aa45f3d4cd32bfdb7395d609132567d772150965cc/data' :
+        'community.wave.seqera.io/library/aria2_rsync:1627a7e9b559cfa0' }"
 
     input:
     val source_url_pdb_mmcif
diff --git a/modules/local/generate_report/environment.yml b/modules/local/generate_report/environment.yml
new file mode 100644
index 00000000..07a5b9f1
--- /dev/null
+++ b/modules/local/generate_report/environment.yml
@@ -0,0 +1,9 @@
+name: generate_report
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - conda-forge::biopython=1.84
+  - conda-forge::matplotlib=3.9.2
+  - conda-forge::pip=24.2
+  - conda-forge::plotly=5.24.1
diff --git a/modules/local/generate_report.nf b/modules/local/generate_report/main.nf
similarity index 72%
rename from modules/local/generate_report.nf
rename to modules/local/generate_report/main.nf
index 3bfdc04e..8ab8fc5d 100644
--- a/modules/local/generate_report.nf
+++ b/modules/local/generate_report/main.nf
@@ -2,10 +2,10 @@ process GENERATE_REPORT {
     tag   "$meta.id-$meta.model"
     label 'process_single'
 
-    conda "bioconda::multiqc:1.21"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/pip_biopython_matplotlib_plotly:e865101a15ad0014' :
-        'community.wave.seqera.io/library/pip_biopython_matplotlib_plotly:4d51afeb4bb75495' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/24/241f0746484727a3633f544c3747bfb77932e1c8c252e769640bd163232d9112/data' :
+        'community.wave.seqera.io/library/biopython_matplotlib_pip_plotly:35975fa0fc54b2d3' }"
 
     input:
     tuple val(meta), path(pdb)
@@ -14,10 +14,10 @@ process GENERATE_REPORT {
     path(template)
 
     output:
-    tuple val(meta), path ("*report.html"), emit: report
+    tuple val(meta), path ("*report.html")     , emit: report
     tuple val(meta), path ("*seq_coverage.png"), optional: true, emit: sequence_coverage
-    tuple val(meta), path ("*_LDDT.html"), emit: plddt
-    path "versions.yml"        , emit: versions
+    tuple val(meta), path ("*_LDDT.html")      , emit: plddt
+    path "versions.yml"                        , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
diff --git a/modules/local/mmseqs_colabfoldsearch.nf b/modules/local/mmseqs_colabfoldsearch/main.nf
similarity index 100%
rename from modules/local/mmseqs_colabfoldsearch.nf
rename to modules/local/mmseqs_colabfoldsearch/main.nf
diff --git a/modules/local/multifasta_to_csv/environment.yml b/modules/local/multifasta_to_csv/environment.yml
new file mode 100644
index 00000000..d92aa27d
--- /dev/null
+++ b/modules/local/multifasta_to_csv/environment.yml
@@ -0,0 +1,7 @@
+name: multifasta_to_csv
+  - conda-forge
+  - bioconda
+dependencies:
+  - conda-forge::grep=3.11
+  - conda-forge::sed=4.8
+  - conda-forge::tar=1.34
diff --git a/modules/local/multifasta_to_csv.nf b/modules/local/multifasta_to_csv/main.nf
similarity index 96%
rename from modules/local/multifasta_to_csv.nf
rename to modules/local/multifasta_to_csv/main.nf
index d5d68fbf..5a737f78 100644
--- a/modules/local/multifasta_to_csv.nf
+++ b/modules/local/multifasta_to_csv/main.nf
@@ -2,7 +2,7 @@ process MULTIFASTA_TO_CSV {
     tag "$meta.id"
     label 'process_single'
 
-    conda "conda-forge::sed=4.7"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
         'nf-core/ubuntu:20.04' }"
diff --git a/modules/local/multifasta_to_singlefasta/environment.yml b/modules/local/multifasta_to_singlefasta/environment.yml
new file mode 100644
index 00000000..273e53dd
--- /dev/null
+++ b/modules/local/multifasta_to_singlefasta/environment.yml
@@ -0,0 +1,8 @@
+name: multifasta_to_singlefasta
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - conda-forge::grep=3.11
+  - conda-forge::sed=4.8
+  - conda-forge::tar=1.34
diff --git a/modules/local/multifasta_to_singlefasta.nf b/modules/local/multifasta_to_singlefasta/main.nf
similarity index 100%
rename from modules/local/multifasta_to_singlefasta.nf
rename to modules/local/multifasta_to_singlefasta/main.nf
diff --git a/modules/local/run_alphafold2.nf b/modules/local/run_alphafold2/main.nf
similarity index 97%
rename from modules/local/run_alphafold2.nf
rename to modules/local/run_alphafold2/main.nf
index f41636a9..6ebd3c1d 100644
--- a/modules/local/run_alphafold2.nf
+++ b/modules/local/run_alphafold2/main.nf
@@ -29,7 +29,7 @@ process RUN_ALPHAFOLD2 {
 
     output:
     path ("${fasta.baseName}*")
-    tuple val(meta), path ("${meta.id}_alphafold2.pdb"), emit: main_pdb
+    tuple val(meta), path ("${meta.id}_alphafold2.pdb")   , emit: top_ranked_pdb
     tuple val(meta), path ("${fasta.baseName}/ranked*pdb"), emit: pdb
     tuple val(meta), path ("${fasta.baseName}/*_msa.tsv") , emit: msa
     tuple val(meta), path ("*_mqc.tsv")                   , emit: multiqc
diff --git a/modules/local/run_alphafold2_msa.nf b/modules/local/run_alphafold2_msa/main.nf
similarity index 97%
rename from modules/local/run_alphafold2_msa.nf
rename to modules/local/run_alphafold2_msa/main.nf
index a4f00676..7428eb7f 100644
--- a/modules/local/run_alphafold2_msa.nf
+++ b/modules/local/run_alphafold2_msa/main.nf
@@ -30,7 +30,7 @@ process RUN_ALPHAFOLD2_MSA {
     output:
     path ("${fasta.baseName}*")
     tuple val(meta), path ("${fasta.baseName}.features.pkl"), emit: features
-    path "versions.yml"                    , emit: versions
+    path "versions.yml"                                     , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
diff --git a/modules/local/run_alphafold2_pred.nf b/modules/local/run_alphafold2_pred/main.nf
similarity index 90%
rename from modules/local/run_alphafold2_pred.nf
rename to modules/local/run_alphafold2_pred/main.nf
index d5e1b9b5..13fb15a7 100644
--- a/modules/local/run_alphafold2_pred.nf
+++ b/modules/local/run_alphafold2_pred/main.nf
@@ -30,11 +30,11 @@ process RUN_ALPHAFOLD2_PRED {
 
     output:
     path ("${fasta.baseName}*")
-    tuple val(meta), path ("${meta.id}_alphafold2.pdb"), emit: main_pdb
+    tuple val(meta), path ("${meta.id}_alphafold2.pdb")   , emit: top_ranked_pdb
     tuple val(meta), path ("${fasta.baseName}/ranked*pdb"), emit: pdb
-    tuple val(meta), path ("*_msa.tsv"), emit: msa
-    tuple val(meta), path ("*_mqc.tsv"), emit: multiqc
-    path "versions.yml", emit: versions
+    tuple val(meta), path ("*_msa.tsv")                   , emit: msa
+    tuple val(meta), path ("*_mqc.tsv")                   , emit: multiqc
+    path "versions.yml"                                   , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
diff --git a/modules/local/run_esmfold.nf b/modules/local/run_esmfold/main.nf
similarity index 96%
rename from modules/local/run_esmfold.nf
rename to modules/local/run_esmfold/main.nf
index 83397be1..9f0478f1 100644
--- a/modules/local/run_esmfold.nf
+++ b/modules/local/run_esmfold/main.nf
@@ -16,7 +16,7 @@ process RUN_ESMFOLD {
     output:
     tuple val(meta), path ("${meta.id}_esmfold.pdb")  , emit: pdb
     tuple val(meta), path ("${meta.id}_plddt_mqc.tsv"), emit: multiqc
-    path "versions.yml", emit: versions
+    path "versions.yml"                               , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
diff --git a/subworkflows/local/post_processing.nf b/subworkflows/local/post_processing.nf
index 631644d7..45d2f0b6 100644
--- a/subworkflows/local/post_processing.nf
+++ b/subworkflows/local/post_processing.nf
@@ -1,5 +1,5 @@
 //
-// Post processing analysis for the predected structures
+// Post processing analysis for the predicted structures
 //
 
 //
@@ -20,9 +20,10 @@ workflow POST_PROCESSING {
 
     take:
     skip_visualisation
+    requested_modes
     requested_modes_size
     ch_report_input
-    ch_proteinfold_template
+    ch_report_template
     ch_comparison_template
     foldseek_search
     ch_foldseek_db
@@ -33,46 +34,54 @@ workflow POST_PROCESSING {
     ch_multiqc_config
     ch_multiqc_custom_config
     ch_multiqc_logo
-    ch_multiqc_custom_methods_description
-    ch_alphafold2_out
-    ch_esmfold_out
-    ch_colabfold_out
+    ch_multiqc_methods_description
+    ch_alphafold2_top_ranked_pdb
+    ch_colabfold_top_ranked_pdb
+    ch_esmfold_top_ranked_pdb
 
     main:
-    ch_comparision_report_files = Channel.empty()
+    ch_comparison_report_files = Channel.empty()
 
     if (!skip_visualisation){
         GENERATE_REPORT(
-            ch_report_input.map{[it[0], it[1]]},
-            ch_report_input.map{[it[0], it[2]]},
-            ch_report_input.map{it[0].model},
-            ch_proteinfold_template
+            ch_report_input.map { [it[0], it[1]] },
+            ch_report_input.map { [it[0], it[2]] },
+            ch_report_input.map { it[0].model },
+            ch_report_template
         )
         ch_versions = ch_versions.mix(GENERATE_REPORT.out.versions)
 
         if (requested_modes_size > 1){
-            ch_comparision_report_files = ch_comparision_report_files.mix(ch_alphafold2_out
+            ch_comparison_report_files = ch_comparison_report_files.mix(ch_alphafold2_top_ranked_pdb
                 .join(GENERATE_REPORT.out.sequence_coverage
-                        .filter{it[0]["model"] == "alphafold2"}
-                        .map{[it[0]["id"], it[1]]}, remainder:true
+                    .filter { it[0]["model"] == "alphafold2" }
+                    .map { [it[0]["id"], it[1]] }, remainder:true
                 )
             )
 
-            ch_comparision_report_files = ch_comparision_report_files.mix(
-                ch_colabfold_out
+            ch_comparison_report_files = ch_comparison_report_files.mix(
+                ch_colabfold_top_ranked_pdb
             )
 
-            ch_comparision_report_files = ch_comparision_report_files.mix(
-                ch_esmfold_out
+            ch_comparison_report_files = ch_comparison_report_files.mix(
+                ch_esmfold_top_ranked_pdb
             )
-            //ch_comparision_report_files.view()
-            ch_comparision_report_files
+
+            ch_comparison_report_files
                 .groupTuple(by: [0], size: requested_modes_size)
-                .set{ch_comparision_report_input}
+                .set { ch_comparison_report_input }
 
             COMPARE_STRUCTURES(
-                ch_comparision_report_input.map{it[1][0]["models"] = params.mode.toLowerCase(); [it[1][0], it[2]]},
-                ch_comparision_report_input.map{it[1][0]["models"] = params.mode.toLowerCase(); [it[1][0], it[3]]},
+                ch_comparison_report_input
+                    .map {
+                        it[1][0]["models"] = requested_modes.toLowerCase();
+                        [ it[1][0], it[2] ]
+                    },
+                ch_comparison_report_input
+                    .map{
+                        it[1][0]["models"] = requested_modes.toLowerCase();
+                        [ it[1][0], it[3] ]
+                    },
                 ch_comparison_template
             )
             ch_versions = ch_versions.mix(COMPARE_STRUCTURES.out.versions)
@@ -82,12 +91,12 @@ workflow POST_PROCESSING {
     if (foldseek_search == "easysearch"){
         FOLDSEEK_EASYSEARCH(
             ch_report_input
-            .map{
-                if (it[0].model == "esmfold")
-                    [it[0], it[1]]
-                else
-                    [it[0], it[1][0]]
-                },
+                .map{
+                    if (it[0].model == "esmfold")
+                        [ it[0], it[1] ]
+                    else
+                        [ it[0], it[1][0] ]
+                    },
             ch_foldseek_db
         )
     }
@@ -98,33 +107,44 @@ workflow POST_PROCESSING {
     softwareVersionsToYAML(ch_versions)
         .collectFile(storeDir: "${outdir}/pipeline_info", name: 'nf_core_proteinfold_software_versions.yml', sort: true, newLine: true)
         .set { ch_collated_versions }
+
     //
     // MODULE: MultiQC
     //
+    ch_multiqc_report = Channel.empty()
+
     if (!skip_multiqc) {
         summary_params           = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
         ch_workflow_summary      = Channel.value(paramsSummaryMultiqc(summary_params))
-        ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
-        ch_methods_description                = Channel.value(methodsDescriptionText(ch_multiqc_custom_methods_description))
+        ch_methods_description   = Channel.value(methodsDescriptionText(ch_multiqc_methods_description))
 
         ch_multiqc_files = Channel.empty()
         ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
         ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml'))
         ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions)
+
         MULTIQC (
-            ch_multiqc_rep.combine(ch_multiqc_files.collect().map{[it]}).map{[it[0], it[1] + it[2]]},
+            ch_multiqc_rep
+                .combine(
+                    ch_multiqc_files
+                        .collect()
+                        .map { [it] }
+                )
+            .map { [ it[0], it[1] + it[2] ] },
             ch_multiqc_config,
-            ch_multiqc_custom_config.collect().ifEmpty([]),
-            ch_multiqc_logo.collect().ifEmpty([]),
+            ch_multiqc_custom_config
+                .collect()
+                .ifEmpty([]),
+            ch_multiqc_logo
+                .collect()
+                .ifEmpty([]),
             [],
             []
         )
         ch_multiqc_report = MULTIQC.out.report.toList()
-    }else{
-        ch_multiqc_report = Channel.empty()
     }
 
     emit:
-    versions   = ch_versions
+    versions       = ch_versions
     multiqc_report = ch_multiqc_report
 }
diff --git a/workflows/alphafold2.nf b/workflows/alphafold2.nf
index 63b6e081..1f5344f5 100644
--- a/workflows/alphafold2.nf
+++ b/workflows/alphafold2.nf
@@ -43,11 +43,11 @@ workflow ALPHAFOLD2 {
     ch_uniprot              // channel: path(uniprot)
 
     main:
-    ch_multiqc_files = Channel.empty()
-    ch_pdb           = Channel.empty()
-    ch_main_pdb      = Channel.empty()
-    ch_msa           = Channel.empty()
-    ch_multiqc_rep   = Channel.empty()
+    ch_multiqc_files  = Channel.empty()
+    ch_pdb            = Channel.empty()
+    ch_top_ranked_pdb = Channel.empty()
+    ch_msa            = Channel.empty()
+    ch_multiqc_report = Channel.empty()
 
     if (alphafold2_model_preset != 'multimer') {
         ch_samplesheet
@@ -78,11 +78,19 @@ workflow ALPHAFOLD2 {
             ch_pdb_seqres,
             ch_uniprot
         )
-        ch_pdb         = ch_pdb.mix(RUN_ALPHAFOLD2.out.pdb)
-        ch_main_pdb    = ch_main_pdb.mix(RUN_ALPHAFOLD2.out.main_pdb)
-        ch_msa         = ch_msa.mix(RUN_ALPHAFOLD2.out.msa)
-        ch_multiqc_rep = RUN_ALPHAFOLD2.out.multiqc.map{it[1]}.toSortedList().map{[["model":"alphafold2"], it]}
-        ch_versions    = ch_versions.mix(RUN_ALPHAFOLD2.out.versions)
+
+        RUN_ALPHAFOLD2
+            .out
+            .multiqc
+            .map { it[1] }
+            .toSortedList()
+            .map { [ [ "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)
+        ch_versions       = ch_versions.mix(RUN_ALPHAFOLD2.out.versions)
 
     } else if (alphafold2_mode == 'split_msa_prediction') {
         //
@@ -121,18 +129,37 @@ workflow ALPHAFOLD2 {
             ch_uniprot,
             RUN_ALPHAFOLD2_MSA.out.features
         )
-        ch_pdb         = ch_pdb.mix(RUN_ALPHAFOLD2_PRED.out.pdb)
-        ch_main_pdb    = ch_main_pdb.mix(RUN_ALPHAFOLD2_PRED.out.main_pdb)
-        ch_msa         = ch_msa.mix(RUN_ALPHAFOLD2_PRED.out.msa)
-        ch_multiqc_rep = RUN_ALPHAFOLD2_PRED.out.multiqc.map{it[1]}.toSortedList().map{[["model":"alphafold2"], it]}
-        ch_versions = ch_versions.mix(RUN_ALPHAFOLD2_PRED.out.versions)
+
+        RUN_ALPHAFOLD2_PRED
+            .out
+            .multiqc
+            .map { it[1] }
+            .toSortedList()
+            .map { [ [ "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)
+        ch_versions       = ch_versions.mix(RUN_ALPHAFOLD2_PRED.out.versions)
     }
 
+    ch_top_ranked_pdb
+        .map { [ it[0]["id"], it[0], it[1] ] }
+        .set { ch_top_ranked_pdb }
+
+    ch_pdb
+        .join(ch_msa)
+        .map {
+            it[0]["model"] = "alphafold2"
+            it
+        }
+        .set { ch_pdb_msa }
+
     emit:
-    main_pdb = ch_main_pdb // channel: /path/to/*.pdb
-    pdb = ch_pdb // channel: /path/to/*.pdb
-    msa = ch_msa // channel: /path/to/*msa.tsv
-    multiqc_report = ch_multiqc_rep // channel: /path/to/multiqc_report.html
+    top_ranked_pdb = ch_top_ranked_pdb // channel: [ id, /path/to/*.pdb ]
+    pdb_msa        = ch_pdb_msa        // channel: [ meta, /path/to/*.pdb, /path/to/*_coverage.png ]
+    multiqc_report = ch_multiqc_report // channel: /path/to/multiqc_report.html
     versions       = ch_versions       // channel: [ path(versions.yml) ]
 }
 
diff --git a/workflows/colabfold.nf b/workflows/colabfold.nf
index c7875cb1..adfa24b6 100644
--- a/workflows/colabfold.nf
+++ b/workflows/colabfold.nf
@@ -35,7 +35,7 @@ workflow COLABFOLD {
     num_recycles           // int: Number of recycles for esmfold
 
     main:
-    ch_multiqc_files = Channel.empty()
+    ch_multiqc_report = Channel.empty()
 
     if (params.colabfold_server == 'webserver') {
         //
@@ -104,14 +104,53 @@ workflow COLABFOLD {
             ch_uniref30,
             num_recycles
         )
-        ch_versions = ch_versions.mix(COLABFOLD_BATCH.out.versions)
+        ch_versions    = ch_versions.mix(COLABFOLD_BATCH.out.versions)
     }
 
+    COLABFOLD_BATCH
+        .out
+        .top_ranked_pdb
+        .map { [ it[0]["id"], it[0], it[1] ] }
+        .join(
+            COLABFOLD_BATCH
+                .out
+                .msa
+                .map { [ it[0]["id"], it[1] ] },
+            remainder:true
+        )
+        .set { ch_top_ranked_pdb }
+
+    COLABFOLD_BATCH
+        .out
+        .pdb
+        .join(COLABFOLD_BATCH.out.msa)
+        .map {
+            it[0]["model"] = "colabfold"
+            it
+        }
+        .set { ch_pdb_msa }
+
+    COLABFOLD_BATCH
+        .out
+        .multiqc
+        .map { it[1] }
+        .toSortedList()
+        .map { [ [ "model":"colabfold"], it.flatten() ] }
+        .set { ch_multiqc_report  }
+
+    COLABFOLD_BATCH
+        .out
+        .multiqc
+
+    COLABFOLD_BATCH
+        .out
+        .multiqc
+        .collect()
+
     emit:
-    pdb = COLABFOLD_BATCH.out.pdb // channel: /path/to/*.pdb
-    main_pdb = COLABFOLD_BATCH.out.main_pdb // channel: /path/to/*.pdb
-    msa = COLABFOLD_BATCH.out.msa // channel: /path/to/*_coverage.png
-    multiqc_report = COLABFOLD_BATCH.out.multiqc.map{it[1]}.flatten().toList().map{[["model":"colabfold"], it]} // channel: /path/to/multiqc_report.html
+    top_ranked_pdb = ch_top_ranked_pdb // channel: [ id, /path/to/*.pdb ]
+    pdb_msa        = ch_pdb_msa        // channel: [ meta, /path/to/*.pdb, /path/to/*_coverage.png ]
+    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
index 57aaa04e..c93c869a 100644
--- a/workflows/esmfold.nf
+++ b/workflows/esmfold.nf
@@ -29,6 +29,7 @@ workflow ESMFOLD {
     ch_versions       // channel: [ path(versions.yml) ]
     ch_esmfold_params // directory: /path/to/esmfold/params/
     ch_num_recycles   // int: Number of recycles for esmfold
+    ch_dummy_file     // channel: [ path(NO_FILE) ]
 
     main:
     ch_multiqc_files = Channel.empty()
@@ -56,9 +57,42 @@ workflow ESMFOLD {
         ch_versions = ch_versions.mix(RUN_ESMFOLD.out.versions)
     }
 
+    RUN_ESMFOLD
+        .out
+        .pdb
+        .combine(ch_dummy_file)
+        .map {
+            it[0]["model"] = "esmfold"
+            [ it[0]["id"], it[0], it[1], it[2] ]
+        }
+        .set { ch_top_ranked_pdb }
+
+    RUN_ESMFOLD
+        .out
+        .multiqc
+        .map { it[1] }
+        .toSortedList()
+        .map { [ [ "model": "esmfold"], it.flatten() ] }
+        .set { ch_multiqc_report  }
+
+    RUN_ESMFOLD
+        .out
+        .pdb
+        .combine(ch_dummy_file)
+        .map {
+            it[0]["model"] = "esmfold"
+            it
+        }
+        .set { ch_pdb_msa }
+
+    ch_pdb_msa
+        .map { [ it[0]["id"], it[0], it[1], it[2] ] }
+        .set { ch_top_ranked_pdb }
+
     emit:
-    pdb =            RUN_ESMFOLD.out.pdb // channel: /path/to/*pdb
-    multiqc_report = RUN_ESMFOLD.out.multiqc.map{it[1]}.toSortedList().map{[["model":"esmfold"], it]}  // channel: /path/to/multiqc_report.html
+    pdb_msa        = ch_pdb_msa          // channel: [ meta, /path/to/*.pdb, dummy_file ]
+    top_ranked_pdb = ch_top_ranked_pdb   // channel: [ id, /path/to/*.pdb ]
+    multiqc_report = ch_multiqc_report   // channel: /path/to/multiqc_report.html
     versions       = ch_versions         // channel: [ path(versions.yml) ]
 }