fhdsl-robot
fhdsl-robot
/ 09-final-workflow.wdl
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May 17, 2024 02:08
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| version 1.0 | |
| ## WDL 101 example workflow | |
| ## | |
| ## This WDL workflow is intended to be used along with the WDL 101 docs. | |
| ## This workflow should be used for inspiration purposes only. | |
| ## | |
| ## We use three samples | |
| ## Samples: | |
| ## MOLM13: Normal sample | |
| ## CALU1: KRAS G12C mutant |
fhdsl-robot
/ 08-final-workflow.wdl
Created
May 17, 2024 02:04
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| version 1.0 | |
| ## WDL 101 example workflow | |
| ## | |
| ## This WDL workflow is intended to be used along with the WDL 101 docs. | |
| ## This workflow should be used for inspiration purposes only. | |
| ## | |
| ## We use three samples | |
| ## Samples: | |
| ## MOLM13: Normal sample | |
| ## CALU1: KRAS G12C mutant |
fhdsl-robot
/ 07-final-workflow.wdl
Created
May 14, 2024 19:48
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| version 1.0 | |
| ## WDL 101 example workflow | |
| ## | |
| ## This WDL workflow is intended to be used along with the WDL 101 docs. | |
| ## This workflow should be used for inspiration purposes only. | |
| ## | |
| ## We use three samples | |
| ## Samples: | |
| ## MOLM13: Normal sample | |
| ## CALU1: KRAS G12C mutant |
fhdsl-robot
/ 06-final-workflow.wdl
Created
May 14, 2024 19:45
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| version 1.0 | |
| struct referenceGenome { | |
| File ref_fasta | |
| File ref_fasta_index | |
| File ref_dict | |
| File ref_amb | |
| File ref_ann | |
| File ref_bwt | |
| File ref_pac |
fhdsl-robot
/ 05-final-workflow.wdl
Created
May 14, 2024 19:43
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| version 1.0 | |
| struct referenceGenome { | |
| File ref_fasta | |
| File ref_fasta_index | |
| File ref_dict | |
| File ref_amb | |
| File ref_ann | |
| File ref_bwt | |
| File ref_pac |
fhdsl-robot
/ 04-final-workflow.wdl
Created
May 14, 2024 19:36
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| version 1.0 | |
| workflow mutation_calling { | |
| input { | |
| File sampleFastq | |
| # Reference genome | |
| File ref_fasta | |
| File ref_fasta_index | |
| File ref_dict |
fhdsl-robot
/ 03-metadata.json
Created
May 14, 2024 19:17
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| { | |
| "mutation_calling.sampleFastq": "/fh/fast/paguirigan_a/pub/ReferenceDataSets/workflow_testing_data/WDL/wdl_101/HCC4006_final.fastq", | |
| "mutation_calling.ref_fasta": "/fh/fast/paguirigan_a/pub/ReferenceDataSets/genome_data/human/hg19/Homo_sapiens_assembly19.fasta", | |
| "mutation_calling.ref_fasta_index": "/fh/fast/paguirigan_a/pub/ReferenceDataSets/genome_data/human/hg19/Homo_sapiens_assembly19.fasta.fai", | |
| "mutation_calling.ref_dict": "/fh/fast/paguirigan_a/pub/ReferenceDataSets/genome_data/human/hg19/Homo_sapiens_assembly19.dict", | |
| "mutation_calling.ref_pac": "/fh/fast/paguirigan_a/pub/ReferenceDataSets/genome_data/human/hg19/Homo_sapiens_assembly19.fasta.pac", | |
| "mutation_calling.ref_sa": "/fh/fast/paguirigan_a/pub/ReferenceDataSets/genome_data/human/hg19/Homo_sapiens_assembly19.fasta.sa", | |
| "mutation_calling.ref_amb": "/fh/fast/paguirigan_a/pub/ReferenceDataSets/genome_data/human/hg19/Homo_sapiens_assembly19.fasta.amb", | |
| "mutation_calling.ref_ann": "/fh/fast/paguirigan_a/pub/ReferenceDataSets/genome_d |
fhdsl-robot
/ 03-final-workflow.wdl
Created
May 14, 2024 19:14
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| version 1.0 | |
| workflow mutation_calling { | |
| input { | |
| File sampleFastq | |
| # Reference genome | |
| File ref_fasta | |
| File ref_fasta_index | |
| File ref_dict |
fhdsl-robot
/ 03-WDL-snippets.wdl
Created
March 13, 2024 16:14
https://github.com/fhdsl/WDL_Workflows_Guide
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| task count_words { | |
| input { | |
| Array[String] a_big_sentence | |
| } | |
| command <<< | |
| ARRAY_OF_WORDS=(~{sep=" " a_big_sentence}) | |
| echo ${#ARRAY_OF_FILES[@]} >> length.txt | |
| # Note how the bash array uses ${} syntax, which could quickly get | |
| # confusing if we used that syntax for our WDL variables. This is | |
| # why we recommend using tilde + {} for your WDL variables. |
fhdsl-robot
/ greetings.wdl
Created
March 13, 2024 16:12
https://github.com/fhdsl/WDL_Workflows_Guide
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| version 1.0 | |
| task greet { | |
| input { | |
| String user | |
| } | |
| command <<< | |
| echo "Hello ~{user}!" > greets.txt | |
| >>> | |
| output { |
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