change cli to remove inputs as options #185
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📝 WalkthroughWalkthroughThe pull request introduces modifications across multiple files in the Harpy project, focusing on command-line argument parsing, workflow file configurations, and output file handling. The primary changes involve updating the Changes
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Actionable comments posted: 0
🧹 Nitpick comments (1)
harpy/bin/inline_to_haplotag.py (1)
13-13: Remove redundantrequired=Trueparameter from positional arguments.The
required=Trueparameter is redundant for positional arguments as they are required by default.Apply this diff to remove the redundant parameter:
-parser.add_argument("forward", required = True, type = str, help = "Forward reads of paired-end FASTQ file pair (gzipped)") -parser.add_argument("reverse", required = True, type = str, help = "Reverse reads of paired-end FASTQ file pair (gzipped)") +parser.add_argument("forward", type = str, help = "Forward reads of paired-end FASTQ file pair (gzipped)") +parser.add_argument("reverse", type = str, help = "Reverse reads of paired-end FASTQ file pair (gzipped)")Also applies to: 17-19
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📒 Files selected for processing (4)
harpy/bin/inline_to_haplotag.py(1 hunks)harpy/snakefiles/simulate_linkedreads.smk(2 hunks)harpy/snakefiles/simulate_snpindel.smk(4 hunks)harpy/snakefiles/simulate_variants.smk(4 hunks)
🔇 Additional comments (10)
harpy/snakefiles/simulate_variants.smk (4)
61-61: LGTM!The changes improve storage efficiency by marking intermediate files as temporary and compressing output files.
Also applies to: 80-80, 84-86
116-117: LGTM!The changes improve storage efficiency by marking intermediate files as temporary.
134-134: LGTM!The changes improve storage efficiency by compressing output files and correctly handle file operations.
Also applies to: 136-142
147-147: LGTM!The changes maintain consistency by updating input file paths to use the compressed file format.
Also applies to: 149-149
harpy/snakefiles/simulate_linkedreads.smk (2)
172-172: LGTM!The command syntax is correctly updated to use positional arguments.
205-205: LGTM!The example command in the workflow summary is correctly updated to reflect the new positional argument format.
harpy/snakefiles/simulate_snpindel.smk (4)
97-97: LGTM!The changes improve storage efficiency by marking intermediate files as temporary.
118-118: LGTM!The changes improve storage efficiency by compressing output files and correctly handle file operations.
Also applies to: 123-128
166-167: LGTM!The changes improve storage efficiency by marking intermediate files as temporary.
186-186: LGTM!The changes improve storage efficiency by compressing output files and correctly handle file operations. The input file paths are correctly updated to maintain consistency.
Also applies to: 188-194, 199-199, 201-201
Summary by CodeRabbit
New Features
inline_to_haplotag.pyscript with simplified argument structureBug Fixes
Refactor
Chores