diff --git a/.test/tasks.py b/.test/tasks.py index 13641a6..f8d90ef 100644 --- a/.test/tasks.py +++ b/.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...") diff --git a/CHANGELOG.md b/CHANGELOG.md index e64f582..f2685e3 100644 --- a/CHANGELOG.md +++ b/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: diff --git a/CITATION.cff b/CITATION.cff index 5992424..899b1f2 100644 --- a/CITATION.cff +++ b/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 diff --git a/workflow/report/material_methods.rst b/workflow/report/material_methods.rst index 27bc6bd..586eab3 100644 --- a/workflow/report/material_methods.rst +++ b/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 diff --git a/workflow/scripts/link_or_concat.py b/workflow/scripts/link_or_concat.py index 3064f53..2d91be9 100644 --- a/workflow/scripts/link_or_concat.py +++ b/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