Open daler opened 1 month ago
I can confirm this is an issue. I was only able to run ./run_complex_test.sh -j16
after removing the LibraryLayout column in ../../test/test_configs/complex-dataset-rnaseq-sampletable.tsv
and replacing it with layout
with SE
in all rows.
My first error message after running ./run_complex_test.sh -j16
without editing the sampletable:
ValueError in file /gpfs/gsfs10/users/NICHD-core0/test/menoldmt/expression-mod/workflows/rnaseq/Snakefile, line 30:
Sampletable appears to be SRA, but no 'Layout' column found. This is required to specify single- or paired-end libraries.
File "/gpfs/gsfs10/users/NICHD-core0/test/menoldmt/expression-mod/workflows/rnaseq/Snakefile", line 30, in <module>
File "/gpfs/gsfs10/users/NICHD-core0/test/menoldmt/expression-mod/workflows/rnaseq/../../lib/patterns_targets.py", line 106, in __init__
File "/gpfs/gsfs10/users/NICHD-core0/test/menoldmt/expression-mod/workflows/rnaseq/../../lib/patterns_targets.py", line 78, in __init__
File "/gpfs/gsfs10/users/NICHD-core0/test/menoldmt/expression-mod/workflows/rnaseq/../../lib/helpers.py", line 20, in detect_layout
File "/gpfs/gsfs10/users/NICHD-core0/test/menoldmt/expression-mod/workflows/rnaseq/../../lib/helpers.py", line 20, in <listcomp>
File "/gpfs/gsfs10/users/NICHD-core0/test/menoldmt/expression-mod/workflows/rnaseq/../../lib/common.py", line 732, in is_paired_end
my second error message after running ./run_complex_test.sh -j16
after adding layout
(even though the initial error message had Layout
):
ValueError in file /gpfs/gsfs10/users/NICHD-core0/test/menoldmt/expression-mod/workflows/rnaseq/Snakefile, line 30:
Expecting column 'layout' or 'LibraryLayout', not both
File "/gpfs/gsfs10/users/NICHD-core0/test/menoldmt/expression-mod/workflows/rnaseq/Snakefile", line 30, in <module>
File "/gpfs/gsfs10/users/NICHD-core0/test/menoldmt/expression-mod/workflows/rnaseq/../../lib/patterns_targets.py", line 106, in __init__
File "/gpfs/gsfs10/users/NICHD-core0/test/menoldmt/expression-mod/workflows/rnaseq/../../lib/patterns_targets.py", line 78, in __init__
File "/gpfs/gsfs10/users/NICHD-core0/test/menoldmt/expression-mod/workflows/rnaseq/../../lib/helpers.py", line 20, in detect_layout
File "/gpfs/gsfs10/users/NICHD-core0/test/menoldmt/expression-mod/workflows/rnaseq/../../lib/helpers.py", line 20, in <listcomp>
File "/gpfs/gsfs10/users/NICHD-core0/test/menoldmt/expression-mod/workflows/rnaseq/../../lib/common.py", line 741, in is_paired_end
To fix this, from here, I removed the original LayoutLibrary
column leaving only the layout
column with SE
in all rows
Recently it seems that the SRA sampletables downloaded from SRA use
Layout
rather thanLibraryLayout
as a column name. This breaks the SRA detection. Confirm this is the case, and make the SRA detection more robust, for example by looking for either of those column names.