search

kfuku52 / amalgkit

RNA-seq data amalgamation for a large-scale evolutionary transcriptomics
BSD 3-Clause "New" or "Revised" License
7 stars 1 forks source link

amalgkit integrate assigns wrong file paths #114

Closed kfuku52 closed 1 year ago

kfuku52 commented 1 year ago

@Hego-CCTB integrate wrongly assign B205 fastq files to the sample B20. I will fix this.

scientific_name curate_group run read1_path read2_path is_sampled is_qualified exclusion lib_layout spot_length total_spots total_bases size private_file
Nicotiana_tabacum Please add B205 /lustre7/home/lustre4/kfuku/my_project/Dirk_Becker/20221229_tobacco_rnaseq/amalgkit_out/input_fastq/B205_2.fastq.gz /lustre7/home/lustre4/kfuku/my_project/Dirk_Becker/20221229_tobacco_rnaseq/amalgkit_out/input_fastq/B205_1.fastq.gz yes yes no paired 150 23152722 6945816600 1900489775 yes
Nicotiana_tabacum Please add B20 /lustre7/home/lustre4/kfuku/my_project/Dirk_Becker/20221229_tobacco_rnaseq/amalgkit_out/input_fastq/B205_2.fastq.gz /lustre7/home/lustre4/kfuku/my_project/Dirk_Becker/20221229_tobacco_rnaseq/amalgkit_out/input_fastq/B205_1.fastq.gz yes yes no paired 150 23152722 6945816600 1900489775 yes
kfuku52 commented 1 year ago

@Hego-CCTB Incorrect use of glob.glob() often invites bugs as I pointed out previously and as identified here. Please avoid it or use as much regex-based limitations as possible when unavoidable.