diff --git a/src/bd_rhapsody/bd_rhapsody_sequence_analysis/test.sh b/src/bd_rhapsody/bd_rhapsody_sequence_analysis/test.sh index 96cf6f09..4cfc95a6 100644 --- a/src/bd_rhapsody/bd_rhapsody_sequence_analysis/test.sh +++ b/src/bd_rhapsody/bd_rhapsody_sequence_analysis/test.sh @@ -64,7 +64,7 @@ cwl-runner \ ############################################# -echo "> Prepare test data" +echo "> Prepare WTA test data" # See structure of reads: # - https://bd-rhapsody-bioinfo-docs.genomics.bd.com/steps/top_steps.html @@ -78,7 +78,7 @@ echo "> Prepare test data" # CLS1 Link CLS2 Link CLS3 UMI # AAAATCCTGT GTGA AACCAAAGT GACA GATAGAGGAG CGCATGTTTATAAC -cat > reads_R1.fastq <<'EOF' +gzip -c > WTAreads_R1.fq.gz <<'EOF' @A00226:970:H5FGVDMXY:1:1101:2645:1000 1:N:0:CAGAGAGG AAAATCCTGTGTGAAACCAAAGTGACAGATAGAGGAGCGCATGTTTATAAC + @@ -93,35 +93,99 @@ EOF # GGATGCCCAGCTAGTTTGAATTTTAGATAAACAACGAATAATTTCGTAGCATAAATATGTCCCAAGCTTAGTTTGGGACATACTTATGCTAAAAAACATTATTGGTTGTTTATCTGAGATTCAGAATTAAGCATTTTAT # note: probably need to reverse it -cat > reads_R2.fastq <<'EOF' +# orig: +# TCTTCGCCCGGCCAGGAATCACAAGCTCCGGGTGGATAAGGCAGCTGCTGCAGCAGCGGCACTACAAGCCA +# AATAATTTCGTAGCATAAATATGTCCCAAGCTTAGTTTGGGACATACTTATGCTAAAAAACATTATTGGTT +gzip -c > WTAreads_R2.fq.gz <<'EOF' @A00226:970:H5FGVDMXY:1:1101:2645:1000 2:N:0:CAGAGAGG -TCTTCGCCCGGCCAGGAATCACAAGCTCCGGGTGGATAAGGCAGCTGCTGCAGCAGCGGCACTACAAGCCA +AGAAGCGGGCCGGTCCTTAGTGTTCGAGGCCCACCTATTCCGTCGACGACGTCGTCGCCGTGATGTTCGGT + FFF:FFF:F:FFFFFFFF,FFFFF:FFF:FFFFFFFFFF,FFFFFFFFFFFFFFF:FFFFFFFFFFF,FFF @A00226:970:H5FGVDMXY:1:1101:2862:1000 2:N:0:CAGAGATG -AATAATTTCGTAGCATAAATATGTCCCAAGCTTAGTTTGGGACATACTTATGCTAAAAAACATTATTGGTT +TTATTAAAGCATCGTATTTATACAGGGTTCGAATCAAACCCTGTATGAATACGATTTTTTGTAATAACCAA + F:FFFF:F,:FFFF,F:FF:F:FFFFFFFF,FF,:FFFFFFFF:FF,,F::FF::FFFFF:F:FFFFF:,F EOF -# gzip -gzip -c reads_R1.fastq > reads_R1.fq.gz -gzip -c reads_R2.fastq > reads_R2.fq.gz +echo "> Prepare ABC test data" +gzip -c > ABCreads_R1.fq.gz <<'EOF' +@A01604:19:HMKLYDRXY:1:1101:2211:1000 1:N:0:CGAGGCTG +CGGTCCAGGGTGAAGGCAGCTAGACAAACAACGCGTGGACTTGTTTTAAAT ++ +FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,F,,: +@A01604:19:HMKLYDRXY:1:1101:2428:1000 1:N:0:CGAGGCTG +AAAGTAACCCGTGAGTACATCTAGACAGTAGAAGCACAAGTTCATTAAATA ++ +FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,,,F: +EOF + +gzip -c > ABCreads_R2.fq.gz <<'EOF' +@A01604:19:HMKLYDRXY:1:1101:2211:1000 2:N:0:CGAGGCTG +NTTAGTGTTCCGTTTGGAGAGTAGCTAGTTGCTGTTCGTGGTCGTTTCAAAAAAAAAAAAAAAAAAAAAAA ++ +#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF, +@A01604:19:HMKLYDRXY:1:1101:2428:1000 2:N:0:CGAGGCTG +NGTACTGCCGGGTAGTAATGTGTTCGTAGCCGGTAATAATCTTCGTGGAAAAAAAAAAAAAAAAAAAAAAA ++ +#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +EOF + +cat > bdabseq_smallpanel.fasta <<'EOF' +>IgM|IGHM|AHS0198|pAbO Catalog_940276 +TTTGGAGGGTAGCTAGTTGCAGTTCGTGGTCGTTTC +>CD19:SJ25C1|CD19|AHS0030|pAbO Catalog_940004 +TAGTAATGTGTTCGTAGCCGGTAATAATCTTCGTGG +>CD278|ICOS|AHS0012|pAbO Catalog_940043 +ATAGTCCGCCGTAATCGTTGTGTCGCTGAAAGGGTT +EOF + +echo "> Prepare SMK test data" + +gzip -c > SMKreads_R1.fq.gz <<'EOF' +@A00226:970:H5FGVDMXY:1:1101:1199:1000 1:N:0:AAGAGGCA +TCAATAGACGAGGTGAAGGTTCGCTGACAAGTCTGTACGTGTTAAACACCA ++ +F:FFFFFFF:FFFFFFFFFFFF,FF,FFFF:FFF:,FFFFFFFF:F,,,F, +@A00226:970:H5FGVDMXY:1:1101:2754:1000 1:N:0:AAGAGGCA +GTTGTACCTTAGTGAGCGACCACCGACAATGGGACTCTCGGACAATTATTT ++ +:FFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF,,:FF +EOF + +gzip -c > SMKreads_R2.fq.gz <<'EOF' +@A00226:970:H5FGVDMXY:1:1101:1199:1000 2:N:0:AAGAGGCA +GTTGTCAAGATGCTACCGTTCAGAGATTCAAGGGCAGCCGCGTCACGATTGGATACGACTGTTGGGACCGG ++ +F,FFF,FFFFF:FFFF:FFF,FF:FFFFFFFFF,FFFFFF,FFFFFFFFFFFFFFF,FFF,FF:F,F,FFF +@A00226:970:H5FGVDMXY:1:1101:2754:1000 2:N:0:AAGAGGCA +GTTGTCAAGATGCTACCGTTCAGAGTGGATGGGATAAGTGCGTGATGGACCGAAGGGACCTCGTGGCCGGA ++ +F:FFFFFFFFFFFFFFFF:FFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF +EOF + ######################################################################################### echo ">> Run $meta_name" "$meta_executable" \ - --reads reads_R1.fq.gz \ - --reads reads_R2.fq.gz \ + --reads WTAreads_R1.fq.gz \ + --reads WTAreads_R2.fq.gz \ + --reads ABCreads_R1.fq.gz \ + --reads ABCreads_R2.fq.gz \ + --reads SMKreads_R1.fq.gz \ + --reads SMKreads_R2.fq.gz \ --reference_archive "$REFERENCE_FILE" \ + --abseq_reference bdabseq_smallpanel.fasta \ --output output \ ${meta_cpus:+---cpus $meta_cpus} \ ${meta_memory_mb:+---memory ${meta_memory_mb}MB} \ --cell_calling_data mRNA \ --exact_cell_count 2 \ --expected_cell_count 2 \ - --exclude_intronic_reads false + --exclude_intronic_reads false \ + --tag_names 1-Jurkat \ + --tag_names 2-Ramos \ + --tag_names 3-THP1 # echo ">> Check if output exists" # assert_file_exists "output.bam"