diff --git a/runs/kallisto/2024-08-05_13-50.log b/runs/kallisto/2024-08-05_13-50.log
new file mode 100644
index 0000000000000000000000000000000000000000..0c3d4588dde5e52748e43bdb92ba6d322bab2851
--- /dev/null
+++ b/runs/kallisto/2024-08-05_13-50.log
@@ -0,0 +1,532 @@
+[1;30mINFO[0m /home/brilator/miniconda3/bin/cwltool 3.1.20240508115724
+[1;30mINFO[0m Resolved '../../workflows/kallisto/kallisto-workflow.cwl' to 'file:///home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/workflows/kallisto/kallisto-workflow.cwl'
+[1;30mINFO[0m [workflow ] start
+[1;30mINFO[0m [workflow ] starting step index
+[1;30mINFO[0m [step index] start
+[1;30mINFO[0m [job index] Using cached output in /home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/c232c80e27f9ac9aff6ffb527ebd4189
+[1;30mINFO[0m [step index] completed success
+[1;30mINFO[0m [workflow ] starting step quant
+[1;30mINFO[0m [step quant] start
+[1;30mINFO[0m [job quant] Output of job will be cached in /home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/04c1d3666d36fb428efa31aedbcef3e7
+[1;30mINFO[0m [job quant] /home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/04c1d3666d36fb428efa31aedbcef3e7$ docker \
+ run \
+ -i \
+ --mount=type=bind,source=/home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/04c1d3666d36fb428efa31aedbcef3e7,target=/gvSNJe \
+ --mount=type=bind,source=/tmp/mbmkyli1,target=/tmp \
+ --mount=type=bind,source=/home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/c232c80e27f9ac9aff6ffb527ebd4189/Talinum.gm.CDS.nt.kallistoIndex,target=/var/lib/cwl/stg2d88a9bc-457d-4cc9-8603-fe974737cab6/Talinum.gm.CDS.nt.kallistoIndex,readonly \
+ --mount=type=bind,source=/home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/assays/Talinum_RNASeq_minimal/dataset/DB_097_CAMMD_CAGATC_L001_R1_001.fastq.gz,target=/var/lib/cwl/stg9989d547-e38c-4bcd-8449-008e2e4a2d83/DB_097_CAMMD_CAGATC_L001_R1_001.fastq.gz,readonly \
+ --workdir=/gvSNJe \
+ --read-only=true \
+ --net=none \
+ --user=1007:1007 \
+ --rm \
+ --cidfile=/tmp/lkq3cvxw/20240805135057-308071.cid \
+ --env=TMPDIR=/tmp \
+ --env=HOME=/gvSNJe \
+ quay.io/biocontainers/kallisto:0.50.1--h6de1650_2 \
+ kallisto \
+ quant \
+ --output-dir \
+ DB_097 \
+ --bootstrap-samples=30 \
+ --fragment-length=200 \
+ --sd \
+ 20 \
+ --index \
+ /var/lib/cwl/stg2d88a9bc-457d-4cc9-8603-fe974737cab6/Talinum.gm.CDS.nt.kallistoIndex \
+ --single \
+ /var/lib/cwl/stg9989d547-e38c-4bcd-8449-008e2e4a2d83/DB_097_CAMMD_CAGATC_L001_R1_001.fastq.gz
+
+[quant] fragment length distribution is truncated gaussian with mean = 200, sd = 20
+[index] k-mer length: 31
+[index] number of targets: 31,434
+[index] number of k-mers: 35,149,253
+[quant] running in single-end mode
+[quant] will process file 1: /var/lib/cwl/stg9989d547-e38c-4bcd-8449-008e2e4a2d83/DB_097_CAMMD_CAGATC_L001_R1_001.fastq.gz
+[quant] finding pseudoalignments for the reads ...
[progress] 1M reads processed (69.4% mapped)
[progress] 2M reads processed (69.3% mapped)
[progress] 3M reads processed (69.2% mapped)
[progress] 4M reads processed (69.3% mapped)
[progress] 5M reads processed (69.2% mapped)
[progress] 6M reads processed (69.2% mapped)
[progress] 7M reads processed (69.2% mapped)
[progress] 8M reads processed (69.2% mapped)
[progress] 9M reads processed (69.2% mapped)
[progress] 10M reads processed (69.2% mapped) done
+[quant] processed 11,071,656 reads, 7,663,833 reads pseudoaligned
+[ em] quantifying the abundances ... done
+[ em] the Expectation-Maximization algorithm ran for 460 rounds
+[bstrp] running EM for the bootstrap: 1
[bstrp] running EM for the bootstrap: 2
[bstrp] running EM for the bootstrap: 3
[bstrp] running EM for the bootstrap: 4
[bstrp] running EM for the bootstrap: 5
[bstrp] running EM for the bootstrap: 6
[bstrp] running EM for the bootstrap: 7
[bstrp] running EM for the bootstrap: 8
[bstrp] running EM for the bootstrap: 9
[bstrp] running EM for the bootstrap: 10
[bstrp] running EM for the bootstrap: 11
[bstrp] running EM for the bootstrap: 12
[bstrp] running EM for the bootstrap: 13
[bstrp] running EM for the bootstrap: 14
[bstrp] running EM for the bootstrap: 15
[bstrp] running EM for the bootstrap: 16
[bstrp] running EM for the bootstrap: 17
[bstrp] running EM for the bootstrap: 18
[bstrp] running EM for the bootstrap: 19
[bstrp] running EM for the bootstrap: 20
[bstrp] running EM for the bootstrap: 21
[bstrp] running EM for the bootstrap: 22
[bstrp] running EM for the bootstrap: 23
[bstrp] running EM for the bootstrap: 24
[bstrp] running EM for the bootstrap: 25
[bstrp] running EM for the bootstrap: 26
[bstrp] running EM for the bootstrap: 27
[bstrp] running EM for the bootstrap: 28
[bstrp] running EM for the bootstrap: 29
[bstrp] running EM for the bootstrap: 30
+
+[1;30mINFO[0m [job quant] Max memory used: 283MiB
+[1;30mINFO[0m [job quant] completed success
+[1;30mINFO[0m [step quant] start
+[1;30mINFO[0m [job quant_2] Output of job will be cached in /home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/ca52501ef3b3047551f9124c1d5004b4
+[1;30mINFO[0m [job quant_2] /home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/ca52501ef3b3047551f9124c1d5004b4$ docker \
+ run \
+ -i \
+ --mount=type=bind,source=/home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/ca52501ef3b3047551f9124c1d5004b4,target=/gvSNJe \
+ --mount=type=bind,source=/tmp/_x8jqxqc,target=/tmp \
+ --mount=type=bind,source=/home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/c232c80e27f9ac9aff6ffb527ebd4189/Talinum.gm.CDS.nt.kallistoIndex,target=/var/lib/cwl/stg19bb2e01-3f1a-4757-8b96-b3736bb62ae2/Talinum.gm.CDS.nt.kallistoIndex,readonly \
+ --mount=type=bind,source=/home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/assays/Talinum_RNASeq_minimal/dataset/DB_099_CAMMD_CTTGTA_L001_R1_001.fastq.gz,target=/var/lib/cwl/stgc8c3c1dc-aa80-4b3c-8c8a-816c343091d2/DB_099_CAMMD_CTTGTA_L001_R1_001.fastq.gz,readonly \
+ --workdir=/gvSNJe \
+ --read-only=true \
+ --net=none \
+ --user=1007:1007 \
+ --rm \
+ --cidfile=/tmp/1q3__lzr/20240805135536-712649.cid \
+ --env=TMPDIR=/tmp \
+ --env=HOME=/gvSNJe \
+ quay.io/biocontainers/kallisto:0.50.1--h6de1650_2 \
+ kallisto \
+ quant \
+ --output-dir \
+ DB_099 \
+ --bootstrap-samples=30 \
+ --fragment-length=200 \
+ --sd \
+ 20 \
+ --index \
+ /var/lib/cwl/stg19bb2e01-3f1a-4757-8b96-b3736bb62ae2/Talinum.gm.CDS.nt.kallistoIndex \
+ --single \
+ /var/lib/cwl/stgc8c3c1dc-aa80-4b3c-8c8a-816c343091d2/DB_099_CAMMD_CTTGTA_L001_R1_001.fastq.gz
+
+[quant] fragment length distribution is truncated gaussian with mean = 200, sd = 20
+[index] k-mer length: 31
+[index] number of targets: 31,434
+[index] number of k-mers: 35,149,253
+[quant] running in single-end mode
+[quant] will process file 1: /var/lib/cwl/stgc8c3c1dc-aa80-4b3c-8c8a-816c343091d2/DB_099_CAMMD_CTTGTA_L001_R1_001.fastq.gz
+[quant] finding pseudoalignments for the reads ...
[progress] 1M reads processed (70.3% mapped)
[progress] 2M reads processed (70.3% mapped)
[progress] 3M reads processed (70.2% mapped)
[progress] 4M reads processed (70.2% mapped)
[progress] 5M reads processed (70.2% mapped)
[progress] 6M reads processed (70.2% mapped)
[progress] 7M reads processed (70.2% mapped)
[progress] 8M reads processed (70.2% mapped)
[progress] 9M reads processed (70.3% mapped)
[progress] 10M reads processed (70.2% mapped)
[progress] 11M reads processed (70.2% mapped)
[progress] 12M reads processed (70.3% mapped)
[progress] 13M reads processed (70.2% mapped) done
+[quant] processed 14,332,278 reads, 10,066,684 reads pseudoaligned
+[ em] quantifying the abundances ... done
+[ em] the Expectation-Maximization algorithm ran for 458 rounds
+[bstrp] running EM for the bootstrap: 1
[bstrp] running EM for the bootstrap: 2
[bstrp] running EM for the bootstrap: 3
[bstrp] running EM for the bootstrap: 4
[bstrp] running EM for the bootstrap: 5
[bstrp] running EM for the bootstrap: 6
[bstrp] running EM for the bootstrap: 7
[bstrp] running EM for the bootstrap: 8
[bstrp] running EM for the bootstrap: 9
[bstrp] running EM for the bootstrap: 10
[bstrp] running EM for the bootstrap: 11
[bstrp] running EM for the bootstrap: 12
[bstrp] running EM for the bootstrap: 13
[bstrp] running EM for the bootstrap: 14
[bstrp] running EM for the bootstrap: 15
[bstrp] running EM for the bootstrap: 16
[bstrp] running EM for the bootstrap: 17
[bstrp] running EM for the bootstrap: 18
[bstrp] running EM for the bootstrap: 19
[bstrp] running EM for the bootstrap: 20
[bstrp] running EM for the bootstrap: 21
[bstrp] running EM for the bootstrap: 22
[bstrp] running EM for the bootstrap: 23
[bstrp] running EM for the bootstrap: 24
[bstrp] running EM for the bootstrap: 25
[bstrp] running EM for the bootstrap: 26
[bstrp] running EM for the bootstrap: 27
[bstrp] running EM for the bootstrap: 28
[bstrp] running EM for the bootstrap: 29
[bstrp] running EM for the bootstrap: 30
+
+[1;30mINFO[0m [job quant_2] Max memory used: 283MiB
+[1;30mINFO[0m [job quant_2] completed success
+[1;30mINFO[0m [step quant] start
+[1;30mINFO[0m [job quant_3] Output of job will be cached in /home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/c4753612931c39e236518d2ca4455d3d
+[1;30mINFO[0m [job quant_3] /home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/c4753612931c39e236518d2ca4455d3d$ docker \
+ run \
+ -i \
+ --mount=type=bind,source=/home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/c4753612931c39e236518d2ca4455d3d,target=/gvSNJe \
+ --mount=type=bind,source=/tmp/0idun1z_,target=/tmp \
+ --mount=type=bind,source=/home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/c232c80e27f9ac9aff6ffb527ebd4189/Talinum.gm.CDS.nt.kallistoIndex,target=/var/lib/cwl/stg4688cdf5-4be9-4a10-a2da-b72109654518/Talinum.gm.CDS.nt.kallistoIndex,readonly \
+ --mount=type=bind,source=/home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/assays/Talinum_RNASeq_minimal/dataset/DB_103_CAMMD_AGTCAA_L001_R1_001.fastq.gz,target=/var/lib/cwl/stg86fb44d0-f2e4-4049-b4ea-b25fb3cc52ce/DB_103_CAMMD_AGTCAA_L001_R1_001.fastq.gz,readonly \
+ --workdir=/gvSNJe \
+ --read-only=true \
+ --net=none \
+ --user=1007:1007 \
+ --rm \
+ --cidfile=/tmp/u2m6ez7p/20240805140121-006110.cid \
+ --env=TMPDIR=/tmp \
+ --env=HOME=/gvSNJe \
+ quay.io/biocontainers/kallisto:0.50.1--h6de1650_2 \
+ kallisto \
+ quant \
+ --output-dir \
+ DB_103 \
+ --bootstrap-samples=30 \
+ --fragment-length=200 \
+ --sd \
+ 20 \
+ --index \
+ /var/lib/cwl/stg4688cdf5-4be9-4a10-a2da-b72109654518/Talinum.gm.CDS.nt.kallistoIndex \
+ --single \
+ /var/lib/cwl/stg86fb44d0-f2e4-4049-b4ea-b25fb3cc52ce/DB_103_CAMMD_AGTCAA_L001_R1_001.fastq.gz
+
+[quant] fragment length distribution is truncated gaussian with mean = 200, sd = 20
+[index] k-mer length: 31
+[index] number of targets: 31,434
+[index] number of k-mers: 35,149,253
+[quant] running in single-end mode
+[quant] will process file 1: /var/lib/cwl/stg86fb44d0-f2e4-4049-b4ea-b25fb3cc52ce/DB_103_CAMMD_AGTCAA_L001_R1_001.fastq.gz
+[quant] finding pseudoalignments for the reads ...
[progress] 1M reads processed (69.0% mapped)
[progress] 2M reads processed (68.9% mapped)
[progress] 3M reads processed (68.9% mapped)
[progress] 4M reads processed (68.9% mapped)
[progress] 5M reads processed (68.9% mapped)
[progress] 6M reads processed (68.9% mapped)
[progress] 7M reads processed (68.9% mapped)
[progress] 8M reads processed (68.9% mapped)
[progress] 9M reads processed (68.9% mapped)
[progress] 10M reads processed (68.9% mapped)
[progress] 11M reads processed (68.9% mapped)
[progress] 12M reads processed (68.9% mapped) done
+[quant] processed 13,083,957 reads, 9,007,909 reads pseudoaligned
+[ em] quantifying the abundances ... done
+[ em] the Expectation-Maximization algorithm ran for 806 rounds
+[bstrp] running EM for the bootstrap: 1
[bstrp] running EM for the bootstrap: 2
[bstrp] running EM for the bootstrap: 3
[bstrp] running EM for the bootstrap: 4
[bstrp] running EM for the bootstrap: 5
[bstrp] running EM for the bootstrap: 6
[bstrp] running EM for the bootstrap: 7
[bstrp] running EM for the bootstrap: 8
[bstrp] running EM for the bootstrap: 9
[bstrp] running EM for the bootstrap: 10
[bstrp] running EM for the bootstrap: 11
[bstrp] running EM for the bootstrap: 12
[bstrp] running EM for the bootstrap: 13
[bstrp] running EM for the bootstrap: 14
[bstrp] running EM for the bootstrap: 15
[bstrp] running EM for the bootstrap: 16
[bstrp] running EM for the bootstrap: 17
[bstrp] running EM for the bootstrap: 18
[bstrp] running EM for the bootstrap: 19
[bstrp] running EM for the bootstrap: 20
[bstrp] running EM for the bootstrap: 21
[bstrp] running EM for the bootstrap: 22
[bstrp] running EM for the bootstrap: 23
[bstrp] running EM for the bootstrap: 24
[bstrp] running EM for the bootstrap: 25
[bstrp] running EM for the bootstrap: 26
[bstrp] running EM for the bootstrap: 27
[bstrp] running EM for the bootstrap: 28
[bstrp] running EM for the bootstrap: 29
[bstrp] running EM for the bootstrap: 30
+
+[1;30mINFO[0m [job quant_3] Max memory used: 283MiB
+[1;30mINFO[0m [job quant_3] completed success
+[1;30mINFO[0m [step quant] start
+[1;30mINFO[0m [job quant_4] Output of job will be cached in /home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/7fa99fa2914046d103fe5e619913fef3
+[1;30mINFO[0m [job quant_4] /home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/7fa99fa2914046d103fe5e619913fef3$ docker \
+ run \
+ -i \
+ --mount=type=bind,source=/home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/7fa99fa2914046d103fe5e619913fef3,target=/gvSNJe \
+ --mount=type=bind,source=/tmp/qdidmi0d,target=/tmp \
+ --mount=type=bind,source=/home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/c232c80e27f9ac9aff6ffb527ebd4189/Talinum.gm.CDS.nt.kallistoIndex,target=/var/lib/cwl/stgd1efd19f-8170-422d-b114-5ea798ac0aec/Talinum.gm.CDS.nt.kallistoIndex,readonly \
+ --mount=type=bind,source=/home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/assays/Talinum_RNASeq_minimal/dataset/DB_161_reC3MD_GTCCGC_L001_R1_001.fastq.gz,target=/var/lib/cwl/stgf263d766-1fa7-41f0-8d5b-d9940c486e06/DB_161_reC3MD_GTCCGC_L001_R1_001.fastq.gz,readonly \
+ --workdir=/gvSNJe \
+ --read-only=true \
+ --net=none \
+ --user=1007:1007 \
+ --rm \
+ --cidfile=/tmp/fx0nz7uo/20240805140646-758938.cid \
+ --env=TMPDIR=/tmp \
+ --env=HOME=/gvSNJe \
+ quay.io/biocontainers/kallisto:0.50.1--h6de1650_2 \
+ kallisto \
+ quant \
+ --output-dir \
+ DB_161 \
+ --bootstrap-samples=30 \
+ --fragment-length=200 \
+ --sd \
+ 20 \
+ --index \
+ /var/lib/cwl/stgd1efd19f-8170-422d-b114-5ea798ac0aec/Talinum.gm.CDS.nt.kallistoIndex \
+ --single \
+ /var/lib/cwl/stgf263d766-1fa7-41f0-8d5b-d9940c486e06/DB_161_reC3MD_GTCCGC_L001_R1_001.fastq.gz
+
+[quant] fragment length distribution is truncated gaussian with mean = 200, sd = 20
+[index] k-mer length: 31
+[index] number of targets: 31,434
+[index] number of k-mers: 35,149,253
+[quant] running in single-end mode
+[quant] will process file 1: /var/lib/cwl/stgf263d766-1fa7-41f0-8d5b-d9940c486e06/DB_161_reC3MD_GTCCGC_L001_R1_001.fastq.gz
+[quant] finding pseudoalignments for the reads ...
[progress] 1M reads processed (71.0% mapped)
[progress] 2M reads processed (70.9% mapped)
[progress] 3M reads processed (70.9% mapped)
[progress] 4M reads processed (70.9% mapped)
[progress] 5M reads processed (70.9% mapped)
[progress] 6M reads processed (70.8% mapped)
[progress] 7M reads processed (70.9% mapped)
[progress] 8M reads processed (70.9% mapped)
[progress] 9M reads processed (70.9% mapped)
[progress] 10M reads processed (70.9% mapped)
[progress] 11M reads processed (70.9% mapped)
[progress] 12M reads processed (70.9% mapped) done
+[quant] processed 12,785,081 reads, 9,058,463 reads pseudoaligned
+[ em] quantifying the abundances ... done
+[ em] the Expectation-Maximization algorithm ran for 500 rounds
+[bstrp] running EM for the bootstrap: 1
[bstrp] running EM for the bootstrap: 2
[bstrp] running EM for the bootstrap: 3
[bstrp] running EM for the bootstrap: 4
[bstrp] running EM for the bootstrap: 5
[bstrp] running EM for the bootstrap: 6
[bstrp] running EM for the bootstrap: 7
[bstrp] running EM for the bootstrap: 8
[bstrp] running EM for the bootstrap: 9
[bstrp] running EM for the bootstrap: 10
[bstrp] running EM for the bootstrap: 11
[bstrp] running EM for the bootstrap: 12
[bstrp] running EM for the bootstrap: 13
[bstrp] running EM for the bootstrap: 14
[bstrp] running EM for the bootstrap: 15
[bstrp] running EM for the bootstrap: 16
[bstrp] running EM for the bootstrap: 17
[bstrp] running EM for the bootstrap: 18
[bstrp] running EM for the bootstrap: 19
[bstrp] running EM for the bootstrap: 20
[bstrp] running EM for the bootstrap: 21
[bstrp] running EM for the bootstrap: 22
[bstrp] running EM for the bootstrap: 23
[bstrp] running EM for the bootstrap: 24
[bstrp] running EM for the bootstrap: 25
[bstrp] running EM for the bootstrap: 26
[bstrp] running EM for the bootstrap: 27
[bstrp] running EM for the bootstrap: 28
[bstrp] running EM for the bootstrap: 29
[bstrp] running EM for the bootstrap: 30
+
+[1;30mINFO[0m [job quant_4] Max memory used: 283MiB
+[1;30mINFO[0m [job quant_4] completed success
+[1;30mINFO[0m [step quant] start
+[1;30mINFO[0m [job quant_5] Output of job will be cached in /home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/6475ad7bb21ae6103cbbd215f880611a
+[1;30mINFO[0m [job quant_5] /home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/6475ad7bb21ae6103cbbd215f880611a$ docker \
+ run \
+ -i \
+ --mount=type=bind,source=/home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/6475ad7bb21ae6103cbbd215f880611a,target=/gvSNJe \
+ --mount=type=bind,source=/tmp/lwmiuppe,target=/tmp \
+ --mount=type=bind,source=/home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/runs/kallisto/cache2/c232c80e27f9ac9aff6ffb527ebd4189/Talinum.gm.CDS.nt.kallistoIndex,target=/var/lib/cwl/stg53b39f3b-5476-4170-8c9a-57684344461d/Talinum.gm.CDS.nt.kallistoIndex,readonly \
+ --mount=type=bind,source=/home/brilator/datahub-dataplant/Facultative-CAM-in-Talinum/assays/Talinum_RNASeq_minimal/dataset/DB_163_reC3MD_GTGAAA_L001_R1_001.fastq.gz,target=/var/lib/cwl/stgba54becd-ad88-446e-971e-7b50ec97640e/DB_163_reC3MD_GTGAAA_L001_R1_001.fastq.gz,readonly \
+ --workdir=/gvSNJe \
+ --read-only=true \
+ --net=none \
+ --user=1007:1007 \
+ --rm \
+ --cidfile=/tmp/jf9xn6l5/20240805141155-698481.cid \
+ --env=TMPDIR=/tmp \
+ --env=HOME=/gvSNJe \
+ quay.io/biocontainers/kallisto:0.50.1--h6de1650_2 \
+ kallisto \
+ quant \
+ --output-dir \
+ DB_163 \
+ --bootstrap-samples=30 \
+ --fragment-length=200 \
+ --sd \
+ 20 \
+ --index \
+ /var/lib/cwl/stg53b39f3b-5476-4170-8c9a-57684344461d/Talinum.gm.CDS.nt.kallistoIndex \
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+[index] k-mer length: 31
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+[index] number of k-mers: 35,149,253
+[quant] running in single-end mode
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+[quant] finding pseudoalignments for the reads ...
[progress] 1M reads processed (70.4% mapped)
[progress] 2M reads processed (70.3% mapped)
[progress] 3M reads processed (70.3% mapped)
[progress] 4M reads processed (70.3% mapped)
[progress] 5M reads processed (70.3% mapped)
[progress] 6M reads processed (70.3% mapped)
[progress] 7M reads processed (70.2% mapped)
[progress] 8M reads processed (70.3% mapped)
[progress] 9M reads processed (70.3% mapped)
[progress] 10M reads processed (70.3% mapped)
[progress] 11M reads processed (70.3% mapped)
[progress] 12M reads processed (70.3% mapped)
[progress] 13M reads processed (70.3% mapped) done
+[quant] processed 14,312,514 reads, 10,054,587 reads pseudoaligned
+[ em] quantifying the abundances ... done
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[bstrp] running EM for the bootstrap: 2
[bstrp] running EM for the bootstrap: 3
[bstrp] running EM for the bootstrap: 4
[bstrp] running EM for the bootstrap: 5
[bstrp] running EM for the bootstrap: 6
[bstrp] running EM for the bootstrap: 7
[bstrp] running EM for the bootstrap: 8
[bstrp] running EM for the bootstrap: 9
[bstrp] running EM for the bootstrap: 10
[bstrp] running EM for the bootstrap: 11
[bstrp] running EM for the bootstrap: 12
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[bstrp] running EM for the bootstrap: 30
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+ --workdir=/gvSNJe \
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+ --output-dir \
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+ --bootstrap-samples=30 \
+ --fragment-length=200 \
+ --sd \
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+ --index \
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+[quant] fragment length distribution is truncated gaussian with mean = 200, sd = 20
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+[quant] finding pseudoalignments for the reads ...
[progress] 1M reads processed (70.0% mapped)
[progress] 2M reads processed (69.8% mapped)
[progress] 3M reads processed (69.8% mapped)
[progress] 4M reads processed (69.8% mapped)
[progress] 5M reads processed (69.8% mapped)
[progress] 6M reads processed (69.8% mapped)
[progress] 7M reads processed (69.8% mapped)
[progress] 8M reads processed (69.8% mapped)
[progress] 9M reads processed (69.8% mapped)
[progress] 10M reads processed (69.8% mapped)
[progress] 11M reads processed (69.8% mapped)
[progress] 12M reads processed (69.8% mapped)
[progress] 13M reads processed (69.8% mapped) done
+[quant] processed 13,679,479 reads, 9,552,610 reads pseudoaligned
+[ em] quantifying the abundances ... done
+[ em] the Expectation-Maximization algorithm ran for 514 rounds
+[bstrp] running EM for the bootstrap: 1
[bstrp] running EM for the bootstrap: 2
[bstrp] running EM for the bootstrap: 3
[bstrp] running EM for the bootstrap: 4
[bstrp] running EM for the bootstrap: 5
[bstrp] running EM for the bootstrap: 6
[bstrp] running EM for the bootstrap: 7
[bstrp] running EM for the bootstrap: 8
[bstrp] running EM for the bootstrap: 9
[bstrp] running EM for the bootstrap: 10
[bstrp] running EM for the bootstrap: 11
[bstrp] running EM for the bootstrap: 12
[bstrp] running EM for the bootstrap: 13
[bstrp] running EM for the bootstrap: 14
[bstrp] running EM for the bootstrap: 15
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[bstrp] running EM for the bootstrap: 18
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[bstrp] running EM for the bootstrap: 21
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[bstrp] running EM for the bootstrap: 26
[bstrp] running EM for the bootstrap: 27
[bstrp] running EM for the bootstrap: 28
[bstrp] running EM for the bootstrap: 29
[bstrp] running EM for the bootstrap: 30
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+[1;30mINFO[0m [job quant_6] completed success
+[1;30mINFO[0m [step quant] completed success
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+}[1;30mINFO[0m Final process status is success
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@@ -1,3 +1,3 @@
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version https://git-lfs.github.com/spec/v1
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index 0f49f0cea5698ec065d580f8fb2f38de0e20c682..f64d715abc232b6b15314dc56bb65b9c879c2fc8 100644
--- a/runs/kallisto/kallisto_results/DB_165/run_info.json
+++ b/runs/kallisto/kallisto_results/DB_165/run_info.json
@@ -1,3 +1,3 @@
version https://git-lfs.github.com/spec/v1
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diff --git a/runs/kallisto/workflow.yml b/runs/kallisto/workflow.yml
index 65f21a57473e05ee98bc6d475a07851b0fad7e38..0f8f15d1452b75328f81888b196b8fd19ac97a11 100644
--- a/runs/kallisto/workflow.yml
+++ b/runs/kallisto/workflow.yml
@@ -34,6 +34,8 @@ InputReadsMultipleSamples:
path: ../../assays/Talinum_RNASeq_minimal/dataset/DB_165_re-C3MD_GTGAAA_L002_R1_001.fastq.gz
format: edam:format_1930 # FASTQ
+numUnderscoresFileName: 2
+
### Kallisto quant Parameters
isSingle: true
FragmentLength: 200
diff --git a/workflows/kallisto/kallisto-help.cwl b/workflows/kallisto/kallisto-help.cwl
index c0dc2d24903c5900802525a7faff3f4b1a0f4d1d..3a05871190f87a7d8436644c9db41b14fa73b758 100644
--- a/workflows/kallisto/kallisto-help.cwl
+++ b/workflows/kallisto/kallisto-help.cwl
@@ -4,15 +4,15 @@ class: CommandLineTool
hints:
DockerRequirement:
- dockerPull: quay.io/biocontainers/kallisto:0.46.2--h4f7b962_1
+ dockerPull: quay.io/biocontainers/kallisto:0.50.1--h6de1650_2
SoftwareRequirement:
packages:
kallisto:
- version: [ "0.46.0" ]
+ version: [ "0.50.0" ]
specs: [ https://identifiers.org/biotools/kallisto ]
inputs: []
-baseCommand: [kallisto, index]
+baseCommand: [kallisto]
outputs: []
\ No newline at end of file
diff --git a/workflows/kallisto/kallisto-index.cwl b/workflows/kallisto/kallisto-index.cwl
index 8813559db52913ca5a937c81c1d1e4438deaeb19..3d29b9edba1ec8b2f5e1033659ecd36f394dba56 100644
--- a/workflows/kallisto/kallisto-index.cwl
+++ b/workflows/kallisto/kallisto-index.cwl
@@ -1,14 +1,14 @@
#!/usr/bin/env cwl-runner
-cwlVersion: v1.0
+cwlVersion: v1.2
class: CommandLineTool
hints:
DockerRequirement:
- dockerPull: quay.io/biocontainers/kallisto:0.46.2--h4f7b962_1
+ dockerPull: quay.io/biocontainers/kallisto:0.50.1--h6de1650_2
SoftwareRequirement:
packages:
kallisto:
- version: [ "0.46.0" ]
+ version: [ "0.50.0" ]
specs: [ https://identifiers.org/biotools/kallisto ]
requirements:
diff --git a/workflows/kallisto/kallisto-quant.cwl b/workflows/kallisto/kallisto-quant.cwl
index 9d6df5f0d6dd8502cecb916830c25685d3e791db..6d3e3578d1e8a43199e2aa18afe8d22888c2f551 100755
--- a/workflows/kallisto/kallisto-quant.cwl
+++ b/workflows/kallisto/kallisto-quant.cwl
@@ -1,14 +1,14 @@
#!/usr/bin/env cwl-runner
-cwlVersion: v1.0
+cwlVersion: v1.2
class: CommandLineTool
hints:
DockerRequirement:
- dockerPull: quay.io/biocontainers/kallisto:0.46.2--h4f7b962_1
+ dockerPull: quay.io/biocontainers/kallisto:0.50.1--h6de1650_2
SoftwareRequirement:
packages:
kallisto:
- version: [ "0.46.0" ]
+ version: [ "0.50.0" ]
specs: [ https://identifiers.org/biotools/kallisto ]
inputs:
diff --git a/workflows/kallisto/kallisto-workflow.cwl b/workflows/kallisto/kallisto-workflow.cwl
index 8a94523cfb5da9490b8862d142be75572740f612..e7f0350801fb853d1dc23a029c2d2f161e00b1c1 100644
--- a/workflows/kallisto/kallisto-workflow.cwl
+++ b/workflows/kallisto/kallisto-workflow.cwl
@@ -14,6 +14,12 @@ inputs:
items:
type: array
items: File
+ # numCharsFileName:
+ # type: int
+ # default: 6
+ numUnderscoresFileName:
+ type: int
+ default: 2
isSingle: boolean
FragmentLength: double?
StandardDeviation: double?
@@ -37,9 +43,13 @@ steps:
scatterMethod: dotproduct
in:
InputReads: InputReadsMultipleSamples
+ # numChars:
+ # source: numCharsFileName
+ numUnderscores: numUnderscoresFileName
QuantOutfolder:
source: InputReadsMultipleSamples
- valueFrom: $(self[0].nameroot.substring(0,6))
+ # valueFrom: $(self[0].nameroot.substring(0, inputs.numChars))
+ valueFrom: $(self[0].nameroot.split('_').slice(0, inputs.numUnderscores).join('_'))
Index: index/index
isSingle: isSingle
FragmentLength: FragmentLength
diff --git a/workflows/kallisto/kallisto_workflow_graph.svg b/workflows/kallisto/kallisto_workflow_graph.svg
index 1eb967f6b8e9bc287fdab50f1c33676a520dd1d1..a9083cee1ed9f5c8f89da0ff9cfcd795b28818aa 100644
--- a/workflows/kallisto/kallisto_workflow_graph.svg
+++ b/workflows/kallisto/kallisto_workflow_graph.svg
@@ -1,161 +1,173 @@
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
"http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
-<!-- Generated by graphviz version 2.50.0 (0)
+<!-- Generated by graphviz version 2.50.0 (20220117.2223)
-->
<!-- Title: G Pages: 1 -->
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- viewBox="0.00 0.00 886.00 395.00" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
+<svg width="1313pt" height="395pt"
+ viewBox="0.00 0.00 1313.00 395.00" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
<g id="graph0" class="graph" transform="scale(1 1) rotate(0) translate(4 391)">
<title>G</title>
-<polygon fill="#eeeeee" stroke="transparent" points="-4,4 -4,-391 882,-391 882,4 -4,4"/>
+<polygon fill="#eeeeee" stroke="transparent" points="-4,4 -4,-391 1309,-391 1309,4 -4,4"/>
<g id="clust1" class="cluster">
<title>cluster_inputs</title>
-<polygon fill="#eeeeee" stroke="black" stroke-dasharray="5,2" points="8,-303 8,-379 870,-379 870,-303 8,-303"/>
-<text text-anchor="middle" x="815" y="-310.8" font-family="Times,serif" font-size="14.00">Workflow Inputs</text>
+<polygon fill="#eeeeee" stroke="black" stroke-dasharray="5,2" points="8,-303 8,-379 1297,-379 1297,-303 8,-303"/>
+<text text-anchor="middle" x="1230" y="-310.8" font-family="Times,serif" font-size="14.00">Workflow Inputs</text>
</g>
<g id="clust2" class="cluster">
<title>cluster_outputs</title>
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-<text text-anchor="middle" x="287.5" y="-15.8" font-family="Times,serif" font-size="14.00">Workflow Outputs</text>
+<polygon fill="#eeeeee" stroke="black" stroke-dasharray="5,2" points="310,-8 310,-84 456,-84 456,-8 310,-8"/>
+<text text-anchor="middle" x="383" y="-15.8" font-family="Times,serif" font-size="14.00">Workflow Outputs</text>
</g>
<!-- quant -->
<g id="node1" class="node">
<title>quant</title>
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