diff --git a/README.md b/README.md index f68716ad..1453b18a 100644 --- a/README.md +++ b/README.md @@ -28,6 +28,21 @@ What we have,now Update ----------------------- +### 2024.12.06 :mystery bugs +When we use `Array[File] renamed_fastq_files = glob("./*_L001_*_001.fastq.gz")` to collect files, it may counter bugs sometimes. As follow message shows, +```plain +workflow run failed: [{"causedBy":[{"causedBy":[{"causedBy":[],"message":"Could not process output, file not found: s3://bioos-wco5n1l5eig44l11sp2sg/analysis/sct8krpqh27m1e54qbrtg/changethename/881c2420-b9fa-41db-8bc4-00f82cf150e8/call-rename_fastq_files_based_on_size/execution/glob-cb37589bd0ab1a6cce9ae3996de17d12/PRJNA543474_dlst000580_SRR9079176_S1_L001_R1_001.fastq.gz*"},{"causedBy":[],"message":"Could not process output, file not found: s3://bioos-wco5n1l5eig44l11sp2sg/analysis/sct8krpqh27m1e54qbrtg/changethename/881c2420-b9fa-41db-8bc4-00f82cf150e8/call-rename_fastq_files_based_on_size/execution/glob-cb37589bd0ab1a6cce9ae3996de17d12/PRJNA543474_dlst000580_SRR9079176_S1_L001_R2_001.fastq.gz*"}],"message":""}],"message":"Workflow failed"}] +``` +It's weird, but I cannot find out why. Then I choose to let `glob` be replaced by `select_all`, as follow code shows, +``` +output{ + File r1 = "${sample_name}_S1_L001_R1_001.fastq.gz" + File r2 = "${sample_name}_S1_L001_R2_001.fastq.gz" + File? i1 = "${sample_name}_S1_L001_I1_001.fastq.gz" + Array[File] renamed_fastq_files = select_all([i1, r1, r2]) +} +``` + ### 2024.10.10 : let's have a try Try using rust as an encapsulation for the command part of the wdl, replacing python.