extend test data

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"