diff --git a/cram-to-bam.inputs.json b/cram-to-bam.inputs.json index a7c9f07..812f1ae 100644 --- a/cram-to-bam.inputs.json +++ b/cram-to-bam.inputs.json @@ -1,8 +1,8 @@ { - "CramToBamFlow.CramToBamTask.sample_name": "NA12878", - "CramToBamFlow.CramToBamTask.input_cram": "gs://gatk-test-data/wgs_cram/NA12878_20k_hg38/NA12878.cram", + "CramToBamFlow.sample_name": "NA12878", + "CramToBamFlow.input_cram": "gs://gatk-test-data/wgs_cram/NA12878_20k_hg38/NA12878.cram", - "CramToBamFlow.CramToBamTask.ref_dict": "gs://genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.dict", - "CramToBamFlow.CramToBamTask.ref_fasta": "gs://genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta", - "CramToBamFlow.CramToBamTask.ref_fasta_index": "gs://genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta.fai" + "CramToBamFlow.ref_dict": "gs://genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.dict", + "CramToBamFlow.ref_fasta": "gs://genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta", + "CramToBamFlow.ref_fasta_index": "gs://genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta.fai" } diff --git a/interleaved-fastq-to-paired-fastq.inputs.json b/interleaved-fastq-to-paired-fastq.inputs.json index 8549141..0d755df 100644 --- a/interleaved-fastq-to-paired-fastq.inputs.json +++ b/interleaved-fastq-to-paired-fastq.inputs.json @@ -1,4 +1,4 @@ { - "UninterleaveFastqs.uninterleave_fqs.input_fastq": "gs://gatk-test-data/wgs_fastq/NA12878_20k/H06JUADXX130110.1.ATCACGAT.20k_interleaved.fastq" + "UninterleaveFastqs.input_fastq": "gs://gatk-test-data/wgs_fastq/NA12878_20k/H06JUADXX130110.1.ATCACGAT.20k_interleaved.fastq" } diff --git a/interleaved-fastq-to-paired-fastq.wdl b/interleaved-fastq-to-paired-fastq.wdl index ea391de..7e253dc 100644 --- a/interleaved-fastq-to-paired-fastq.wdl +++ b/interleaved-fastq-to-paired-fastq.wdl @@ -13,8 +13,15 @@ version 1.0 ################## workflow UninterleaveFastqs { + input { + File input_fastq + } - call uninterleave_fqs + + call uninterleave_fqs { + input: + input_fastq = input_fastq + } }