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workflow_STAR.csv
We can make this file beautiful and searchable if this error is corrected: It looks like row 16 should actually have 3 columns, instead of 4 in line 15.
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workflow_STAR.csv
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step,protocol,dependencies
s00a_TrimReads_FastQC,protocols/TrimReads_TrimGalore.sh,
s00b_CombineFastq,protocols/CombineFastq.sh,s00a_TrimReads_FastQC
s01_STAR,protocols/STAR.sh,s00b_CombineFastq
s02_AddOrReplaceReadGroups,protocols/AddOrReplaceReadGroups.sh,s01_STAR
s03_MergeBam,protocols/MergeBam.sh,s02_AddOrReplaceReadGroups
s04_MarkDuplicates,protocols/MarkDuplicates.sh,s03_MergeBam
s05_Stranded,protocols/Stranded.sh,s04_MarkDuplicates
s06a_QCStats,protocols/QCStats.sh,s05_Stranded
s06b_TIN,protocols/TIN.sh,s05_Stranded
s06c_RNASeQC,protocols/RNASeQC.sh,s05_Stranded
s06d_RNASeQCPlots,protocols/RNASeQCPlots.sh,s06c_RNASeQC
s07a_HTSeq_count,protocols/HTSeq_count.sh,s05_Stranded
s07b_Design,protocols/Design.sh,s07a_HTSeq_count
s07c_MakeExpressionTable,protocols/MakeExpressionTable.sh,s07b_Design
s07d_DE_deseq2,protocols/DE.sh,s07b_Design,s07c_MakeExpressionTable
s08a_Leafcutter_intron_clustering,protocols/Leafcutter_intron_clustering.sh,s07b_Design
s08b_Leafcutter_rare,protocols/Leafcutter_rare.sh,s08a_Leafcutter_intron_clustering
s08c_Leafcutter,protocols/Leafcutter.sh,s05_Stranded;s08a_Leafcutter_intron_clustering
s08d_Leafcutter_filter,protocols/Leafcutter_filter.sh,s08b_Leafcutter_rare
s09a_rMATs,protocols/rMATs.sh,s05_Stranded;s07b_Design
s09b_rMats_reformat,protocols/rMats_reformat.sh,s09a_rMATs
s09c_rMATs_DE,protocols/rMATs_DE.sh,s08c_Leafcutter
s09d_rMats_reformat_DE,protocols/rMats_reformat_DE.sh,s09c_rMATs_DE
s10a_normalize_SJ,protocols/normalize_SJ.sh,s07b_Design
s10b_create_SJDB,protocols/create_SJDB.sh,s10a_normalize_SJ
s10c_annotate_SJ_with_SJDB,protocols/annotate_SJ_with_SJDB.sh,s10b_create_SJDB
s11a_SplitAndTrim,protocols/SplitAndTrim.sh,s04_MarkDuplicates
s11b_BQSR,protocols/BQSR.sh,s12a_SplitAndTrim
s11c_GatkHaplotypeCallerGvcf,protocols/GatkHaplotypeCallerGvcf.sh,s12b_BQSR
s11d_GatkGenotypeGvcf,protocols/GatkGenotypeGvcf.sh,s12c_GatkHaplotypeCallerGvcf
s12_MultiQCReport,protocols/MultiQCReport.sh,s7c_MakeExpressionTable;s06a_QCStats;s06b_TIN
s13_MakeCondordanceVcf,protocols/MakeCondordanceVcf.sh,s03_MergeBam
s14_CopyToResultsDir,protocols/CopyToResultsDir.sh,s07c_MakeExpressionTable;s09d_rMats_reformat_DE.sh;s12d_GatkGenotypeGvcf;s14_MultiQCReport;s07d_DE_deseq2;s08d_Leafcutter_filter