Layout rather than LibraryLayout

[daler]

Recently it seems that the SRA sampletables downloaded from SRA use Layout rather than LibraryLayout 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.

[menoldmt]

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.

[menoldmt]

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