nf-core · ieduba · May 25, 2026 · May 25, 2026 · May 25, 2026 · May 25, 2026
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,13 +7,16 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Added`
 
+- Update saltshaker classification reporting by adding customer ID to samples' reports and displaying them as tabs in html [#856](https://github.com/nf-core/raredisease/pull/856)
+
 ### `Changed`
 
 - Replace `ch_publish`/`subworkflow_results` with named typed channel emits for annotate_rhocallviz and annotate_genome_snvs subworkflows [#858](https://github.com/nf-core/raredisease/pull/858)
 - Expand annotate_rhocallviz test with snapshot assertions [#858](https://github.com/nf-core/raredisease/pull/858)
 - Refactor scatter_genome subworkflow: alias GAWK as `GENOME_FAI_TO_BED`, remove `val_save_reference` parameter, move interval flattening into `annotate_genome_snvs` [#857](https://github.com/nf-core/raredisease/pull/857)
 - Replace `ch_publish`/`subworkflow_results` with named typed channel emits for qc_bam subworkflow [#853](https://github.com/nf-core/raredisease/pull/853)
 - Replace `ch_publish`/`subworkflow_results` with named typed channel emits for alignment and subsample-MT subworkflows [#850](https://github.com/nf-core/raredisease/pull/850)
+- Update saltshaker modules to version 1.1.1 so they can run on empty mitosalt output [#856](https://github.com/nf-core/raredisease/pull/856)
 
 ### `Fixed`
 

diff --git a/bin/saltshaker_to_html.py b/bin/saltshaker_to_html.py
@@ -0,0 +1,95 @@
+#!/usr/bin/env python3
+import re
+import typer
+from pathlib import Path
+from typing import List, Optional
+
+CSS = """.tabcontent { display: none; }
+.tabcontent.active { display: block; }
+.tablinks { padding: 12px 20px; cursor: pointer; background-color: #f1f1f1; border: 1px solid #ccc; }
+.tablinks.active { background-color: #4CAF50; color: white; }
+.tablinks:hover { background-color: #ddd; }
+"""
+
+JS = """
+function openTab(evt, tabName) {
+    var i, tabcontent, tablinks;
+    tabcontent = document.getElementsByClassName("tabcontent");
+    for (i = 0; i < tabcontent.length; i++) {
+        tabcontent[i].classList.remove("active");
+    }
+    tablinks = document.getElementsByClassName("tablinks");
+    for (i = 0; i < tablinks.length; i++) {
+        tablinks[i].classList.remove("active");
+    }
+    document.getElementById(tabName).classList.add("active");
+    evt.currentTarget.classList.add("active");
+}
+document.getElementsByClassName("tablinks")[0].click();
+"""
+
+def txt_to_html(txt_file):
+    with open(txt_file) as tf:
+        content = tf.read()
+    html_content = re.sub(r'\\n', '<br>', content)
+    return html_content
+
+def create_tab_button(sample_id):
+    return f'''<button class="tablinks" onclick="openTab(event, '{sample_id}')">{sample_id}</button>\n'''
+
+def create_tab_content(sample_id, txt_file):
+    html_content = txt_to_html(txt_file)
+    return f'''<div id="{sample_id}" class="tabcontent">
+\t<h3>{sample_id}</h3>
+\t<pre style="padding: 15px; border-radius: 5px; overflow-x: auto;">{html_content}</pre>
+</div>
+'''
+
+app = typer.Typer()
+
+@app.command()
+def main(
+    input: List[Path] = typer.Option(
+        ...,
+        "--input",
+        exists=True,
+        file_okay=True,
+        dir_okay=False,
+        help="Path to input .txt file (can be multiple)"
+    ),
+    sample: List[str] = typer.Option(
+        ...,
+        "--sample",
+        help="Sample ID(s) corresponding to the input .txt file(s)"
+    ),
+    output: Path = typer.Option(
+        ...,
+        "--output",
+        help="Path to output .html file"
+    )
+):
+    tab_buttons = ''.join(create_tab_button(sid) for sid in sample)
+    tab_contents = ''.join(create_tab_content(sid, inp) for inp, sid in zip(input, sample))
+
+    html = f"""<html>
+<head>
+<style>
+{CSS}
+</style>
+</head>
+<body>
+<div class="tab">
+{tab_buttons}
+</div>
+{tab_contents}
+<script>
+{JS}
+</script>
+</body>
+</html>"""
+
+    with open(output, 'w') as f:
+        f.write(html)
+
+if __name__ == "__main__":
+    app()
diff --git a/conf/modules/call_sv_MT.config b/conf/modules/call_sv_MT.config
@@ -37,6 +37,10 @@ process {
         ].join(' ') }
     }
 
+    withName: '.*CALL_SV_MT:SALTSHAKER_TO_HTML' {
+        ext.prefix = { "${meta.id}.saltshaker_classify" }
+    }
+
     withName: '.*CALL_SV_MT:SALTSHAKER_PLOT' {
         ext.args = '--blacklist --genes'
     }

diff --git a/conf/test.config b/conf/test.config
@@ -1,7 +1,7 @@
 /*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     Nextflow config file for running minimal tests
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     Defines input files and everything required to run a fast and simple pipeline test.
 
     Use as follows:

diff --git a/modules.json b/modules.json
@@ -156,11 +156,6 @@
                         "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                         "installed_by": ["modules"]
                     },
-                    "find/concatenate": {
-                        "branch": "master",
-                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
-                        "installed_by": ["modules"]
-                    },
                     "gatk4/bedtointervallist": {
                         "branch": "master",
                         "git_sha": "a89928b3f8b4fa91e4c783e769dbc10f91c89b32",
@@ -388,17 +383,17 @@
                     },
                     "saltshaker/call": {
                         "branch": "master",
-                        "git_sha": "9d051963759dda1a424374e23f4f22aaa2b0bd60",
+                        "git_sha": "0932567705843eb10831d31cb200ea3f69a2322e",
                         "installed_by": ["modules"]
                     },
                     "saltshaker/classify": {
                         "branch": "master",
-                        "git_sha": "ff5f2ad4481a4a1e1769a1fad922681e7f7fd176",
+                        "git_sha": "a61c82ad6d255d555aa6c7f1c3c0e90c3735c830",
                         "installed_by": ["modules"]
                     },
                     "saltshaker/plot": {
                         "branch": "master",
-                        "git_sha": "ff5f2ad4481a4a1e1769a1fad922681e7f7fd176",
+                        "git_sha": "a61c82ad6d255d555aa6c7f1c3c0e90c3735c830",
                         "installed_by": ["modules"]
                     },
                     "sambamba/depth": {

diff --git a/modules/local/saltshaker_to_html/environment.yml b/modules/local/saltshaker_to_html/environment.yml
@@ -0,0 +1,5 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - conda-forge::typer=0.25.1
diff --git a/modules/local/saltshaker_to_html/main.nf b/modules/local/saltshaker_to_html/main.nf
@@ -2,27 +2,25 @@ process SALTSHAKER_TO_HTML {
     tag "$meta.id"
     label "process_low"
 
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a2/a23c958d5a0439419f82069df6217c542f6ab13816f9808ed73307dff1efe227/data':
+        'community.wave.seqera.io/library/typer:0.25.1--25ea8a9ce34456a3' }"
+
     input:
-    tuple val(meta), path(classify)
+    tuple val(meta), path(saltshaker_classify_reports), val(sample_ids)
 
     output:
     tuple val(meta), path("*.html"), emit: classify_html
 
     script:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def args = task.ext.args ?: ""
     """
-    python3 << 'EOF'
-    import re
-    def saltshaker_txt_to_html(txt_file):
-        with open(txt_file) as f:
-            content = f.read()
-        html_content = re.sub(r'\\n', '<br>', content)
-        return html_content
-
-    html = saltshaker_txt_to_html("${classify}")
-    with open("${classify.baseName}.saltshaker_classify.html", 'w') as f:
-        f.write('<html><body>')
-        f.write(f'<pre style="padding: 15px; border-radius: 5px; overflow-x: auto;">{html}</pre>')
-        f.write('</body></html>')
-    EOF
+    saltshaker_to_html.py \
+        $args \
+        --input ${saltshaker_classify_reports.join(' --input ')} \
+        --sample ${sample_ids.join(' --sample ')} \
+        --output ${prefix}.html
     """
 }
diff --git a/modules/nf-core/find/concatenate/environment.yml b/modules/nf-core/find/concatenate/environment.yml
diff --git a/modules/nf-core/find/concatenate/main.nf b/modules/nf-core/find/concatenate/main.nf