Path	Lines of Code
CHANGELOG.md	45
CODE_OF_CONDUCT.md	4
CONTRIBUTING.md	59
README.md	140
examples/demo-nextflow-project/agc-project.yaml	27
examples/demo-nextflow-project/workflows/hello/main.nf	11
examples/demo-nextflow-project/workflows/rnaseq/MANIFEST.json	7
examples/demo-nextflow-project/workflows/rnaseq/inputs.json	5
examples/demo-nextflow-project/workflows/rnaseq/options.json	5
examples/demo-wdl-project/agc-project.yaml	43
examples/demo-wdl-project/workflows/haplotype/MANIFEST.json	6
examples/demo-wdl-project/workflows/haplotype/haplotypecaller-gvcf-gatk4.hg38.wgs.inputs.json	8
examples/demo-wdl-project/workflows/haplotype/haplotypecaller-gvcf-gatk4.wdl	234
examples/demo-wdl-project/workflows/hello/hello.wdl	11
examples/demo-wdl-project/workflows/read/main.wdl	21
examples/demo-wdl-project/workflows/read/read.inputs.json	3
examples/demo-wdl-project/workflows/words/MANIFEST.json	6
examples/demo-wdl-project/workflows/words/words-with-vowels.inputs.json	3
examples/demo-wdl-project/workflows/words/words-with-vowels.wdl	27
examples/gatk-best-practices-project-miniwdl/README.md	4
examples/gatk-best-practices-project-miniwdl/agc-project.yaml	69
examples/gatk-best-practices-project-miniwdl/gatk4-basic-joint-genotyping/MANIFEST.json	7
examples/gatk-best-practices-project-miniwdl/gatk4-basic-joint-genotyping/gatk4-basic-joint-genotyping.inputs.json	12
examples/gatk-best-practices-project-miniwdl/gatk4-basic-joint-genotyping/gatk4-basic-joint-genotyping.wdl	264
examples/gatk-best-practices-project-miniwdl/gatk4-data-processing/MANIFEST.json	7
examples/gatk-best-practices-project-miniwdl/gatk4-data-processing/processing-for-variant-discovery-gatk4.hg38.wgs.inputs.json	25
examples/gatk-best-practices-project-miniwdl/gatk4-data-processing/processing-for-variant-discovery-gatk4.wdl	653
examples/gatk-best-practices-project-miniwdl/gatk4-germline-snps-indels/MANIFEST.json	7
examples/gatk-best-practices-project-miniwdl/gatk4-germline-snps-indels/haplotypecaller-gvcf-gatk4.hg38.wgs.inputs.json	8
examples/gatk-best-practices-project-miniwdl/gatk4-germline-snps-indels/haplotypecaller-gvcf-gatk4.wdl	232
examples/gatk-best-practices-project-miniwdl/gatk4-rnaseq-germline-snps-indels/MANIFEST.json	5
examples/gatk-best-practices-project-miniwdl/gatk4-rnaseq-germline-snps-indels/gatk4-rnaseq-germline-snps-indels.inputs.json	17
examples/gatk-best-practices-project-miniwdl/gatk4-rnaseq-germline-snps-indels/gatk4-rnaseq-germline-snps-indels.wdl	716
examples/gatk-best-practices-project-miniwdl/seq-format-conversions/bam-to-unmapped-bams/MANIFEST.json	7
examples/gatk-best-practices-project-miniwdl/seq-format-conversions/bam-to-unmapped-bams/bam-to-unmapped-bams.inputs.json	3
examples/gatk-best-practices-project-miniwdl/seq-format-conversions/bam-to-unmapped-bams/bam-to-unmapped-bams.wdl	117
examples/gatk-best-practices-project-miniwdl/seq-format-conversions/cram-to-bam/MANIFEST.json	7
examples/gatk-best-practices-project-miniwdl/seq-format-conversions/cram-to-bam/cram-to-bam.inputs.json	7
examples/gatk-best-practices-project-miniwdl/seq-format-conversions/cram-to-bam/cram-to-bam.wdl	133
examples/gatk-best-practices-project-miniwdl/seq-format-conversions/interleaved-fastq-to-paired-fastq/MANIFEST.json	7
examples/gatk-best-practices-project-miniwdl/seq-format-conversions/interleaved-fastq-to-paired-fastq/interleaved-fastq-to-paired-fastq.inputs.json	3
examples/gatk-best-practices-project-miniwdl/seq-format-conversions/interleaved-fastq-to-paired-fastq/interleaved-fastq-to-paired-fastq.wdl	46
examples/gatk-best-practices-project-miniwdl/seq-format-conversions/paired-fastq-to-unmapped-bam/MANIFEST.json	7
examples/gatk-best-practices-project-miniwdl/seq-format-conversions/paired-fastq-to-unmapped-bam/paired-fastq-to-unmapped-bam.wdl	146
examples/gatk-best-practices-project-miniwdl/seq-format-conversions/paired-fastq-to-unmapped-bam/paired-fastq-to-unmapped-inputs.json	12
examples/gatk-best-practices-project-miniwdl/seq-format-validation/MANIFEST.json	7
examples/gatk-best-practices-project-miniwdl/seq-format-validation/validate-bam.wdl	80
examples/gatk-best-practices-project-miniwdl/seq-format-validation/validate-bams.input.json	6
examples/gatk-best-practices-project/README.md	21
examples/gatk-best-practices-project/agc-project.yaml	69
examples/gatk-best-practices-project/gatk4-basic-joint-genotyping/MANIFEST.json	7
examples/gatk-best-practices-project/gatk4-basic-joint-genotyping/gatk4-basic-joint-genotyping.inputs.json	12
examples/gatk-best-practices-project/gatk4-basic-joint-genotyping/gatk4-basic-joint-genotyping.wdl	264
examples/gatk-best-practices-project/gatk4-basic-joint-genotyping/options.json	4
examples/gatk-best-practices-project/gatk4-data-processing/MANIFEST.json	7
examples/gatk-best-practices-project/gatk4-data-processing/options.json	4
examples/gatk-best-practices-project/gatk4-data-processing/processing-for-variant-discovery-gatk4.hg38.wgs.inputs.json	25
examples/gatk-best-practices-project/gatk4-data-processing/processing-for-variant-discovery-gatk4.wdl	653
examples/gatk-best-practices-project/gatk4-germline-snps-indels/MANIFEST.json	7
examples/gatk-best-practices-project/gatk4-germline-snps-indels/haplotypecaller-gvcf-gatk4.hg38.wgs.inputs.json	8
examples/gatk-best-practices-project/gatk4-germline-snps-indels/haplotypecaller-gvcf-gatk4.wdl	232
examples/gatk-best-practices-project/gatk4-germline-snps-indels/options.json	4
examples/gatk-best-practices-project/gatk4-rnaseq-germline-snps-indels/MANIFEST.json	5
examples/gatk-best-practices-project/gatk4-rnaseq-germline-snps-indels/gatk4-rnaseq-germline-snps-indels.inputs.json	17
examples/gatk-best-practices-project/gatk4-rnaseq-germline-snps-indels/gatk4-rnaseq-germline-snps-indels.wdl	716
examples/gatk-best-practices-project/gatk4-rnaseq-germline-snps-indels/options.json	4
examples/gatk-best-practices-project/seq-format-conversions/bam-to-unmapped-bams/MANIFEST.json	7
examples/gatk-best-practices-project/seq-format-conversions/bam-to-unmapped-bams/bam-to-unmapped-bams.inputs.json	3
examples/gatk-best-practices-project/seq-format-conversions/bam-to-unmapped-bams/bam-to-unmapped-bams.wdl	117
examples/gatk-best-practices-project/seq-format-conversions/bam-to-unmapped-bams/options.json	4
examples/gatk-best-practices-project/seq-format-conversions/cram-to-bam/MANIFEST.json	7
examples/gatk-best-practices-project/seq-format-conversions/cram-to-bam/cram-to-bam.inputs.json	7
examples/gatk-best-practices-project/seq-format-conversions/cram-to-bam/cram-to-bam.wdl	133
examples/gatk-best-practices-project/seq-format-conversions/cram-to-bam/options.json	4
examples/gatk-best-practices-project/seq-format-conversions/interleaved-fastq-to-paired-fastq/MANIFEST.json	7
examples/gatk-best-practices-project/seq-format-conversions/interleaved-fastq-to-paired-fastq/interleaved-fastq-to-paired-fastq.inputs.json	3
examples/gatk-best-practices-project/seq-format-conversions/interleaved-fastq-to-paired-fastq/interleaved-fastq-to-paired-fastq.wdl	46
examples/gatk-best-practices-project/seq-format-conversions/interleaved-fastq-to-paired-fastq/options.json	4
examples/gatk-best-practices-project/seq-format-conversions/paired-fastq-to-unmapped-bam/MANIFEST.json	7
examples/gatk-best-practices-project/seq-format-conversions/paired-fastq-to-unmapped-bam/options.json	4
examples/gatk-best-practices-project/seq-format-conversions/paired-fastq-to-unmapped-bam/paired-fastq-to-unmapped-bam.wdl	146
examples/gatk-best-practices-project/seq-format-conversions/paired-fastq-to-unmapped-bam/paired-fastq-to-unmapped-inputs.json	12
examples/gatk-best-practices-project/seq-format-validation/MANIFEST.json	7
examples/gatk-best-practices-project/seq-format-validation/options.json	4
examples/gatk-best-practices-project/seq-format-validation/validate-bam.wdl	80
examples/gatk-best-practices-project/seq-format-validation/validate-bams.input.json	6
examples/nf-core-project/README.md	17
examples/nf-core-project/agc-project.yaml	62
examples/nf-core-project/workflows/atacseq/MANIFEST.json	7
examples/nf-core-project/workflows/atacseq/inputs.json	5
examples/nf-core-project/workflows/rnaseq/MANIFEST.json	5
examples/nf-core-project/workflows/rnaseq/inputs.json	4
examples/nf-core-project/workflows/sarek/MANIFEST.json	7
examples/nf-core-project/workflows/sarek/inputs.json	3
extras/agc-minimal-permissions/README.md	16
extras/agc-minimal-permissions/cdk.json	17
extras/agc-minimal-permissions/package-lock.json	11246
extras/agc-minimal-permissions/package.json	28
extras/agc-minimal-permissions/tsconfig.json	23
package-lock.json	3
packages/cdk/README.md	3
packages/cdk/apps/context/cdk.json	6
packages/cdk/apps/core/cdk.json	6
packages/cdk/go.mod	2
packages/cdk/lib/wes_adapter/README.md	19
packages/cdk/lib/wes_adapter/rest_api/workflow/input.json	4
packages/cdk/npm-shrinkwrap.json	7369
packages/cdk/package.json	34
packages/cdk/tsconfig.json	23
packages/cli/TESTING.md	21
packages/cli/go.mod	39
packages/cli/internal/pkg/cli/spec/project_schema.json	144
packages/engines/cromwell/README.md	22
packages/engines/cromwell/aws-cromwell-updates.patch	1463
packages/engines/miniwdl/README.md	19
packages/engines/nextflow/README.md	19
packages/engines/snakemake/README.md	35
packages/wes_api/client/README.md	33
packages/wes_api/client/go.mod	7
scripts/package-lock.json	2735
scripts/package.json	5
site/README.md	54
site/archetypes/default.md	5
site/content/en/community/_index.md	19
site/content/en/search.md	4
site/package-lock.json	2286
site/package.json	24
version.json	3