mvdbeek 003cf64326 Fix comp1 / test_subworkflow_map_over_data_column

2025-10-01 16:05:01 +02:00

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gff

Add missing stuff pointed out in code review

2025-09-25 17:40:08 +02:00

__init__.py

Check types of modules without type annotations in the their signatures on new modules.

2021-10-11 16:08:26 -04:00

axt_to_concat_fasta.py

Enable flake8-comprehensions ruff rules

2024-03-09 19:11:20 +00:00

axt_to_concat_fasta.xml

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axt_to_fasta.py

Apply black to tools as well

2022-02-03 09:12:13 -05:00

axt_to_fasta.xml

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axt_to_lav_code.py

Apply black to tools as well

2022-02-03 09:12:13 -05:00

axt_to_lav.py

Drop unnecessary global statements

2025-04-05 09:55:42 +02:00

axt_to_lav.xml

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bed2gff.xml

Add missing stuff pointed out in code review

2025-09-25 17:40:08 +02:00

bed_to_bigbed.xml

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bed_to_gff_converter.py

Apply black to tools as well

2022-02-03 09:12:13 -05:00

catWrapper.xml

Add coreutils requirement to cat1

2025-09-25 17:38:37 +02:00

changeCase.pl

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changeCase.xml

Add missing requirements to perl tools

2023-09-29 15:22:09 +02:00

commWrapper.pl

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commWrapper.xml

Add missing requirements to perl tools

2023-09-29 15:22:09 +02:00

compare.xml

Fix comp1 / test_subworkflow_map_over_data_column

2025-10-01 16:05:01 +02:00

condense_characters.pl

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condense_characters.xml

Add missing requirements to perl tools

2023-09-29 15:22:09 +02:00

convert_characters.py

FileInput no longer accept 'U' in the file mode

2023-09-16 18:33:07 +02:00

convert_characters.xml

Add required_files

2025-09-25 17:38:36 +02:00

CreateInterval.pl

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CreateInterval.xml

Add missing requirements to perl tools

2023-09-29 15:22:09 +02:00

cutWrapper.pl

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cutWrapper.xml

Add missing requirements to perl tools

2023-09-29 15:22:09 +02:00

fileGrep.xml

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fixedValueColumn.pl

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fixedValueColumn.xml

Use format_source="input" instead of format="input"

2023-01-13 10:58:57 +01:00

gff2bed.xml

Add missing stuff pointed out in code review

2025-09-25 17:40:08 +02:00

gff_to_bed_converter.py

Fix type annotations

2025-02-09 01:54:55 +00:00

grep_1.0.1.xml

Add missing stuff pointed out in code review

2025-09-25 17:40:08 +02:00

grep.xml

Change grep test pattern and restore assertions

2025-09-25 17:56:35 +02:00

gtf2bedgraph.xml

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gtf_to_bedgraph_converter.py

Apply black to tools as well

2022-02-03 09:12:13 -05:00

headWrapper.xml

Bump wrapper version and declare updates to it WF-safe

2022-10-31 23:03:32 +01:00

join.py

Apply black to tools as well

2022-02-03 09:12:13 -05:00

joiner2.xml

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joiner.xml

Add missing stuff pointed out in code review

2025-09-25 17:40:08 +02:00

lav_to_bed_code.py

Replace file_name property with get_file_name function

2023-11-08 17:17:14 -05:00

lav_to_bed.py

Apply black to tools as well

2022-02-03 09:12:13 -05:00

lav_to_bed.xml

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mergeCols.py

Apply black to tools as well

2022-02-03 09:12:13 -05:00

mergeCols.xml

Add required_files

2025-09-25 17:38:36 +02:00

pasteWrapper.xml

Modernize Paste1, drop perl wrapper

2025-09-25 17:38:35 +02:00

random_lines_two_pass.py

Apply black to tools as well

2022-02-03 09:12:13 -05:00

randomlines.py

Apply black to tools as well

2022-02-03 09:12:13 -05:00

randomlines.xml

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remove_beginning.xml

Add missing stuff pointed out in code review

2025-09-25 17:40:08 +02:00

secure_hash_message_digest.py

Apply black to tools as well

2022-02-03 09:12:13 -05:00

secure_hash_message_digest.xml

Make hash selection mandatory

2021-02-22 11:13:02 +01:00

sff_extract.py

Drop unnecessary global statements

2025-04-05 09:55:42 +02:00

sff_extractor.xml

Fix `sff_extract` tool, drop type annotation

2022-03-16 15:24:55 +01:00

sorter.xml

Skip set -e

2025-10-01 09:57:10 +02:00

tailWrapper.xml

Apply suggestions from code review

2021-05-04 13:47:29 +02:00

trimmer.py

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2022-02-03 09:12:13 -05:00

trimmer.xml

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ucsc_gene_bed_to_exon_bed.py

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2022-02-03 09:12:13 -05:00

ucsc_gene_bed_to_exon_bed.xml

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ucsc_gene_bed_to_intron_bed.py

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2022-02-03 09:12:13 -05:00

ucsc_gene_bed_to_intron_bed.xml

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ucsc_gene_table_to_intervals.py

Apply black to tools as well

2022-02-03 09:12:13 -05:00

ucsc_gene_table_to_intervals.xml

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uniq.py

Apply black to tools as well

2022-02-03 09:12:13 -05:00

uniq.xml

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wc_gnu.xml

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wig_to_bigwig.xml

hide wig_to_bigWig tool

2024-02-15 11:38:05 +01:00

wiggle_to_simple.py

Apply black to tools as well

2022-02-03 09:12:13 -05:00

wiggle_to_simple.xml

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