2.5.1

.test/tasks.py

@@ -45,12 +45,14 @@ def get_latest_release(
     future: str = future_version,
     known: str | None = None,
 ) -> str:
-    if address.split("/")[-1] == op.basename(op.dirname(os.getcwd())):
-        print(f"Current pipeline detected, using {future=}...")
+    name = address.split("/")[-1]
+    current_name = op.basename(op.dirname(os.getcwd()))
+    if name == current_name:
+        print(f"Current pipeline detected, using {future=} for {name=}...")
         return get_future_version(changelog=locations["changelog"])
 
     if known is not None:
-        print(f"Known version provided {known=}")
+        print(f"Known version provided {known=} for {name=}")
         return known
 
     print(f"Seaching for {address=} on github...")

CHANGELOG.md

@@ -1,3 +1,9 @@
+# 2.5.1
+
+## Fix:
+
+* Allow fastq to be untouchable from current node (iRODS, cold-storage, ...)
+
 # 2.5.0
 
 ## Features:

CITATION.cff

@@ -7,4 +7,4 @@ date-released: '2024-12-13'
 message: If you use this software, please cite it as below.
 title: fair-fastqc-multiqc
 url: https://github.com/tdayris/fair_fastqc_multiqc
-version: 2.5.0
+version: 2.5.1

workflow/report/material_methods.rst

@@ -42,4 +42,4 @@ and relies on fair_genome_indexer_ [#fair_genome_indexer_quote]_ pipeline.
 :Authors:
     Thibault Dayris
 
-:Version: 2.5.0 of 2024-12-13
+:Version: 2.5.1 of 2024-12-13

workflow/scripts/link_or_concat.py

@@ -244,7 +244,10 @@ def copy_or_concat(
         f"concatenated, linked, or copied to {dest=}, knowing {cold_storage=}"
     )
     if not os.path.exists(src):
-        raise FileNotFoundError(f"Could not find source at: {src=}")
+        if not (src.startswith(cold_storage) or src.startswith(irods_prefix)):
+            raise FileNotFoundError(f"Could not find local source at: {src=}")
+        # Case src is on irods of cold-storage and only availabl on login-node.
+    # Case src exists.
 
     src_sep: str | None = None
     src_len: int = 1