Copy all the .command.sh scripts used in nfcore pipeline run to current directory

gistfile1.txt

$ cut -f 2,4 ../execution_trace.txt | grep -v ^hash | perl -pe 's/ \(\S+\)$/.sh/' | tr : _ | while IFS=$'\t' read -r -a myarray; do dir=${myarray[0]}; process=${myarray[1]}; cp -v ../../../work/"$dir"*/.command.sh $process; done
‘../../../work/fd/f407a60eb791dbe1b0cd5a2f4d0da2/.command.sh’ -> ‘RNASEQ_INPUT_CHECK_SAMPLESHEET_CHECK.sh’
‘../../../work/19/a3f9ef62792935a4e8f3452bedb915/.command.sh’ -> ‘RNASEQ_CAT_FASTQ.sh’
‘../../../work/9d/f6079c32bdaa9471dcfc52e826b0e0/.command.sh’ -> ‘RNASEQ_PREPARE_GENOME_GTF2BED.sh’
‘../../../work/a1/96ca0e62620ea4e682fdd8096ee46a/.command.sh’ -> ‘RNASEQ_PREPARE_GENOME_GET_CHROM_SIZES.sh’
‘../../../work/76/5335dbfa3241ec59fafc25d9abc7de/.command.sh’ -> ‘RNASEQ_PREPARE_GENOME_GTF_GENE_FILTER.sh’
‘../../../work/e2/523c975ead28b5181984ff7d64e5f3/.command.sh’ -> ‘RNASEQ_PREPARE_GENOME_RSEM_PREPAREREFERENCE_TRANSCRIPTS.sh’
‘../../../work/c7/c8ffe7adc5ad790aa2fe6608b114eb/.command.sh’ -> ‘RNASEQ_FASTQC_UMITOOLS_TRIMGALORE_FASTQC.sh’
‘../../../work/89/7b23e5e3ef8e6cf43a67fb7480277c/.command.sh’ -> ‘RNASEQ_PREPARE_GENOME_STAR_GENOMEGENERATE.sh’
‘../../../work/02/5bef85ad3dfb22a776fc7598ca6dc5/.command.sh’ -> ‘RNASEQ_FASTQC_UMITOOLS_TRIMGALORE_TRIMGALORE.sh’
‘../../../work/40/de5934699ab07b83c02ddbaff0c9eb/.command.sh’ -> ‘RNASEQ_ALIGN_STAR_STAR_ALIGN.sh’
‘../../../work/4f/9a15225f3afdd566ec3293d1b4fbfd/.command.sh’ -> ‘RNASEQ_ALIGN_STAR_BAM_SORT_SAMTOOLS_SAMTOOLS_SORT.sh’
‘../../../work/26/6926d21b2b30a90e8671bade789286/.command.sh’ -> ‘RNASEQ_QUANTIFY_STAR_SALMON_SALMON_QUANT.sh’
‘../../../work/d8/f73746d0e15ade80176997355b9a49/.command.sh’ -> ‘RNASEQ_ALIGN_STAR_BAM_SORT_SAMTOOLS_SAMTOOLS_INDEX.sh’
‘../../../work/56/78c52b1fa38ce372442904e142c3ce/.command.sh’ -> ‘RNASEQ_ALIGN_STAR_BAM_SORT_SAMTOOLS_BAM_STATS_SAMTOOLS_SAMTOOLS_IDXSTATS.sh’
‘../../../work/14/48cc7eac93529d4525ed3bad3b0863/.command.sh’ -> ‘RNASEQ_QUANTIFY_STAR_SALMON_SALMON_TX2GENE.sh’
‘../../../work/08/11a2d6cc86b7acca21b977fe66f508/.command.sh’ -> ‘RNASEQ_ALIGN_STAR_BAM_SORT_SAMTOOLS_BAM_STATS_SAMTOOLS_SAMTOOLS_FLAGSTAT.sh’
‘../../../work/8c/d4e0b462caf25ab3b6a468289d85f6/.command.sh’ -> ‘RNASEQ_QUANTIFY_STAR_SALMON_SALMON_TXIMPORT.sh’
‘../../../work/e9/104105ac34f19ab74eaa027de84c5a/.command.sh’ -> ‘RNASEQ_QUANTIFY_STAR_SALMON_SALMON_MERGE_COUNTS’
‘../../../work/c7/8e8e38a94ddfe40b7b68e090b96c91/.command.sh’ -> ‘RNASEQ_QUANTIFY_STAR_SALMON_SALMON_SE_GENE.sh’
‘../../../work/0b/bede7bf83f31b81e195f3b0bebdbf6/.command.sh’ -> ‘RNASEQ_QUANTIFY_STAR_SALMON_SALMON_SE_GENE_LENGTH_SCALED.sh’
‘../../../work/2b/495366017c302f396b02c18f2cb7b7/.command.sh’ -> ‘RNASEQ_QUANTIFY_STAR_SALMON_SALMON_SE_GENE_SCALED.sh’
‘../../../work/34/79b2b703de8b61909d04441ff23648/.command.sh’ -> ‘RNASEQ_QUANTIFY_STAR_SALMON_SALMON_SE_TRANSCRIPT.sh’
‘../../../work/65/820f0fb454c6fcc9ca91b0e98fe8d2/.command.sh’ -> ‘RNASEQ_DESEQ2_QC_STAR_SALMON’
‘../../../work/c4/1aa2c29569f9871870cce0e8637448/.command.sh’ -> ‘RNASEQ_ALIGN_STAR_BAM_SORT_SAMTOOLS_BAM_STATS_SAMTOOLS_SAMTOOLS_STATS.sh’
‘../../../work/24/8f7cc55346c3a7847e448837c1af52/.command.sh’ -> ‘RNASEQ_MARK_DUPLICATES_PICARD_PICARD_MARKDUPLICATES.sh’
‘../../../work/77/5c8028dc41a4aac3ca839709f1539e/.command.sh’ -> ‘RNASEQ_RSEQC_RSEQC_INFEREXPERIMENT.sh’
‘../../../work/38/dfc7ea2c9366dd790795b151dcf725/.command.sh’ -> ‘RNASEQ_MULTIQC_CUSTOM_STRAND_CHECK’
‘../../../work/fd/f52049786111be794dc719f2f80ab3/.command.sh’ -> ‘RNASEQ_MARK_DUPLICATES_PICARD_SAMTOOLS_INDEX.sh’
‘../../../work/37/3a82767c2e4fa84ada11ea1240ae49/.command.sh’ -> ‘RNASEQ_RSEQC_RSEQC_INNERDISTANCE.sh’
‘../../../work/13/d9e68fc399b55059376d637d949f99/.command.sh’ -> ‘RNASEQ_MARK_DUPLICATES_PICARD_BAM_STATS_SAMTOOLS_SAMTOOLS_IDXSTATS.sh’
‘../../../work/a9/4b122582033c053b29f8fb27f5a4eb/.command.sh’ -> ‘RNASEQ_MARK_DUPLICATES_PICARD_BAM_STATS_SAMTOOLS_SAMTOOLS_FLAGSTAT.sh’
‘../../../work/51/6443df1132601442efc8411aeabeb4/.command.sh’ -> ‘RNASEQ_SUBREAD_FEATURECOUNTS.sh’
‘../../../work/78/ed2aa9e42a38a58decd957cff16c05/.command.sh’ -> ‘RNASEQ_MULTIQC_CUSTOM_BIOTYPE.sh’
‘../../../work/78/c53255079d79d4ccb50b14678f9374/.command.sh’ -> ‘RNASEQ_PRESEQ_LCEXTRAP.sh’
‘../../../work/70/9a445ed2204f0d4c77744c56e3a75d/.command.sh’ -> ‘RNASEQ_MARK_DUPLICATES_PICARD_BAM_STATS_SAMTOOLS_SAMTOOLS_STATS.sh’
‘../../../work/b8/64b465863b05c3d8bc76c403d2cd61/.command.sh’ -> ‘RNASEQ_BEDTOOLS_GENOMECOV.sh’
‘../../../work/2f/5608e8f807fa7269e3e7ba8ccb8d78/.command.sh’ -> ‘RNASEQ_UCSC_BEDCLIP.sh’
‘../../../work/32/d317e3fa6106c45a1f2809daf3f7b2/.command.sh’ -> ‘RNASEQ_UCSC_BEDGRAPHTOBIGWIG.sh’
‘../../../work/7c/2108ac59ade83e81e9745ad6de341b/.command.sh’ -> ‘RNASEQ_RSEQC_RSEQC_JUNCTIONANNOTATION.sh’
‘../../../work/ec/999b5f15bcf3eca4289444fc5de67f/.command.sh’ -> ‘RNASEQ_RSEQC_RSEQC_BAMSTAT.sh’
‘../../../work/b6/38345f223d588c8b845e2401c48874/.command.sh’ -> ‘RNASEQ_RSEQC_RSEQC_JUNCTIONSATURATION.sh’
‘../../../work/d7/68ccfd694c8d5bd506c93c29b027ce/.command.sh’ -> ‘RNASEQ_RSEQC_RSEQC_READDISTRIBUTION.sh’
‘../../../work/4d/bd8742aef8ba801ed6f74c1b9e0b67/.command.sh’ -> ‘RNASEQ_RSEQC_RSEQC_READDUPLICATION.sh’
‘../../../work/ad/1503cbb24e3ad5c4a296eb0b013f1f/.command.sh’ -> ‘RNASEQ_DUPRADAR.sh’
‘../../../work/95/14b30826f620ec210c6773ed2cb04e/.command.sh’ -> ‘RNASEQ_STRINGTIE.sh’
‘../../../work/17/e1d4c37bd3bb0aa2284728e6350942/.command.sh’ -> ‘RNASEQ_GET_SOFTWARE_VERSIONS’
‘../../../work/c3/7b2f4d49aecb508bfdc895bb0f0ff2/.command.sh’ -> ‘RNASEQ_MULTIQC.sh’