nf-core · MatthiasZepper · Jul 7, 2025 · Jun 18, 2025 · Jun 18, 2025 · Jun 18, 2025
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -43,6 +43,7 @@
 - Update pre-commit hook astral-sh/ruff-pre-commit to v0.12.1 ([#3648](https://github.com/nf-core/tools/pull/3648))
 - Update error message for rocrate_readme_sync ([#3652](https://github.com/nf-core/tools/pull/3652))
 - Update `nf-core modules info` command after `meta.yml` restructuring ([#3659](https://github.com/nf-core/tools/pull/3659))
+- Enable parsing of multi-line config values ([#3629](https://github.com/nf-core/tools/pull/3629))
 
 ## [v3.3.1 - Tungsten Tamarin Patch](https://github.com/nf-core/tools/releases/tag/3.3.1) - [2025-06-02]
 

diff --git a/nf_core/pipelines/download.py b/nf_core/pipelines/download.py
@@ -892,7 +892,9 @@ def rectify_raw_container_matches(self, raw_findings):
             """
             direct_match = re.match(either_url_or_docker, container_value.strip())
             if direct_match:
-                cleaned_matches.append(direct_match.group(0))
+                # eliminate known false positives also from direct matches
+                if direct_match.group(0) not in ["singularity", "apptainer"]:
+                    cleaned_matches.append(direct_match.group(0))
                 continue  # oh yes, that was plain sailing
 
             """

diff --git a/nf_core/utils.py b/nf_core/utils.py
@@ -325,13 +325,21 @@ def fetch_wf_config(wf_path: Path, cache_config: bool = True) -> dict:
     result = run_cmd("nextflow", f"config -flat {wf_path}")
     if result is not None:
         nfconfig_raw, _ = result
-        for line in nfconfig_raw.splitlines():
-            ul = line.decode("utf-8")
-            try:
-                k, v = ul.split(" = ", 1)
-                config[k] = v.strip("'\"")
-            except ValueError:
-                log.debug(f"Couldn't find key=value config pair:\n  {ul}")
+        nfconfig = nfconfig_raw.decode("utf-8")
+        multiline_key_value_pattern = re.compile(r"(^|\n)([^\n=]+?)\s*=\s*((?:(?!\n[^\n=]+?\s*=).)*)", re.DOTALL)
+
+        for config_match in multiline_key_value_pattern.finditer(nfconfig):
+            k = config_match.group(2).strip()
+            v = config_match.group(3).strip().strip("'\"")
+            if k and v == "":
+                config[k] = "null"
+                log.debug(f"Config key: {k}, value: empty string")
+            elif k and v:
+                config[k] = v
+                log.debug(f"Config key: {k}, value: {v}")
+            else:
+                log.debug(f"Couldn't find key=value config pair:\n  {config_match.group(0)}")
+            del config_match
 
     # Scrape main.nf for additional parameter declarations
     # Values in this file are likely to be complex, so don't both trying to capture them. Just get the param name.
@@ -341,8 +349,9 @@ def fetch_wf_config(wf_path: Path, cache_config: bool = True) -> dict:
             for line in fh:
                 line_str = line.decode("utf-8")
                 match = re.match(r"^\s*(params\.[a-zA-Z0-9_]+)\s*=(?!=)", line_str)
-                if match:
+                if match and match.group(1):
                     config[match.group(1)] = "null"
+
     except FileNotFoundError as e:
         log.debug(f"Could not open {main_nf} to look for parameter declarations - {e}")
 

diff --git a/tests/data/mock_config_containers/nextflow.config b/tests/data/mock_config_containers/nextflow.config
@@ -26,4 +26,12 @@ process {
         container = { "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/r-shinyngs:1.7.1--r42hdfd78af_1':'quay.io/biocontainers/r-shinyngs:1.7.1--r42hdfd78af_1' }" }
     }
 
+    // example from nf-core/pairgenomealign 2.2.0
+
+    withName:'ALIGNMENT_.*' {
+        container = { "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+            'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/06/06beccfa4d48e5daf30dd8cee4f7e06fd51594963db0d5087ab695365b79903b/data' :
+            'community.wave.seqera.io/library/last_samtools_open-fonts:176a6ab0c8171057'}" }
+    }
+
 }
diff --git a/tests/pipelines/test_download.py b/tests/pipelines/test_download.py
@@ -221,22 +221,30 @@ def test__find_container_images_config_nextflow(self, tmp_path, mock_fetch_wf_co
         if result is not None:
             nfconfig_raw, _ = result
             config = {}
-            for line in nfconfig_raw.splitlines():
-                ul = line.decode("utf-8")
-                try:
-                    k, v = ul.split(" = ", 1)
-                    config[k] = v.strip("'\"")
-                except ValueError:
-                    pass
+            nfconfig = nfconfig_raw.decode("utf-8")
+            multiline_key_value_pattern = re.compile(r"(^|\n)([^\n=]+?)\s*=\s*((?:(?!\n[^\n=]+?\s*=).)*)", re.DOTALL)
+
+            for match in multiline_key_value_pattern.finditer(nfconfig):
+                k = match.group(2).strip()
+                v = match.group(3).strip().strip("'\"")
+                if k and v:
+                    config[k] = v
             mock_fetch_wf_config.return_value = config
             download_obj.find_container_images("workflow")
-            assert len(download_obj.containers) == 4
             assert "nfcore/methylseq:1.0" in download_obj.containers
             assert "nfcore/methylseq:1.4" in download_obj.containers
             assert "nfcore/sarek:dev" in download_obj.containers
             assert (
                 "https://depot.galaxyproject.org/singularity/r-shinyngs:1.7.1--r42hdfd78af_1" in download_obj.containers
             )
+            assert (
+                "https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/06/06beccfa4d48e5daf30dd8cee4f7e06fd51594963db0d5087ab695365b79903b/data"
+                in download_obj.containers
+            )
+            assert (
+                "community.wave.seqera.io/library/last_samtools_open-fonts:176a6ab0c8171057" in download_obj.containers
+            )
+            assert "singularity" not in download_obj.containers
             # does not yet pick up nfcore/sarekvep:dev.${params.genome}, because that is no valid URL or Docker URI.
 
     #