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epigen / scifiRNA-seq

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input-bam-glob issue #9

Open somnathtagore opened 3 years ago

nvelthuijs commented 2 years ago

Hi Somnath,

Did you erase your message because you fixed the issue? If so, could you perhaps share if you remember what you did to fix this? I'm running into the same issue:

(scifi)nvelthuijs@cn45:/scratch/nvelthuijs/scifi$ scifi map -c trial_exp/config.yaml -o trial_exp/output —-input_bam_glob trial_exp/demultiplexed/demulti2-4/*.bam trail_exp/experiment_annotation.csv
scifi:pipeline:L141 (main) [INFO] > scifi-RNA-seq pipeline
usage: scifi map [-h] [--arrayed] [--array-size ARRAY_SIZE] [-d] [-t] [-s SAMPLE_SUBSET] [-c CONFIG_FILE] [-o ROOT_OUTPUT_DIR] --input-bam-glob
                 INPUT_BAM_GLOB
                 sample_annotation
scifi map: error: the following arguments are required: --input-bam-glob

Thanks!