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Merge pull request #31 from ghga-de/27-rearrange-source-requirements
27 rearrange source requirements
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@@ -138,7 +138,7 @@ Note that some form of configuration will be needed so that Nextflow knows how t | |
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**control**: The path to the control file, if there is no control will be kept blank. | ||
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**contro*index***: The path to the control index file, if there is no control will be kept blank. | ||
**control_index***: The path to the control index file, if there is no control will be kept blank. | ||
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## Data Requirements | ||
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@@ -178,6 +178,8 @@ All VCF and BED files need to be indexed with tabix and should be in the same fo | |
- UCSC Phast Cons Elements (bed) | ||
- UCSC Encode TFBS (bed) | ||
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NOTE: The reference set bundle which is used in PCAWG study can be found and downloaded [here](https://dcc.icgc.org/api/v1/download?fn=/PCAWG/reference_data/pcawg-dkfz/dkfz-workflow-dependencies_150318_0951.tar.gz). (NOTE: only in hg19) | ||
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## Documentation | ||
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The nf-snvcalling pipeline comes with documentation about the pipeline [usage](https://github.com/ghga-de/nf-snvcalling/blob/main/docs/usage.md) and [output](https://github.com/ghga-de/nf-snvcalling/blob/main/docs/output.md). | ||
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@@ -195,7 +197,7 @@ The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium. | |
Nature volume 578, pages 82–93 (2020). | ||
DOI 10.1038/s41586-020-1969-6 | ||
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We tank the following people for their extensive assistance in the development of this pipeline: | ||
We thank the following people for their extensive assistance in the development of this pipeline: | ||
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Nagarajan Paramasivam (@NagaComBio) [[email protected]](mailto:[email protected]) | ||
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sample,tumor,tumor_index,control,control_index | ||
SEQC2_LL1,/omics/odcf/analysis/OE0526_projects/public_data_analyses/seqc2/sequencing/exon_sequencing/results_per_pid/SEQC2_LL1/alignment_hg38/tumor01_SEQC2_LL1_merged.mdup.bam,/omics/odcf/analysis/OE0526_projects/public_data_analyses/seqc2/sequencing/exon_sequencing/results_per_pid/SEQC2_LL1/alignment_hg38/tumor01_SEQC2_LL1_merged.mdup.bam.bai,/omics/odcf/analysis/OE0526_projects/public_data_analyses/seqc2/sequencing/exon_sequencing/results_per_pid/SEQC2_LL1/alignment_hg38/control01_SEQC2_LL1_merged.mdup.bam,/omics/odcf/analysis/OE0526_projects/public_data_analyses/seqc2/sequencing/exon_sequencing/results_per_pid/SEQC2_LL1/alignment_hg38/control01_SEQC2_LL1_merged.mdup.bam.bai |
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sample,tumor,tumor_index,control,control_index | ||
SEQC2_LL1,/omics/odcf/analysis/OE0526_projects/public_data_analyses/seqc2/sequencing/whole_genome_sequencing/results_per_pid/SEQC2_LL1/alignment/tumor01_SEQC2_LL1_merged.mdup.bam,/omics/odcf/analysis/OE0526_projects/public_data_analyses/seqc2/sequencing/whole_genome_sequencing/results_per_pid/SEQC2_LL1/alignment/tumor01_SEQC2_LL1_merged.mdup.bam.bai,/omics/odcf/analysis/OE0526_projects/public_data_analyses/seqc2/sequencing/whole_genome_sequencing/results_per_pid/SEQC2_LL1/alignment/control01_SEQC2_LL1_merged.mdup.bam,/omics/odcf/analysis/OE0526_projects/public_data_analyses/seqc2/sequencing/whole_genome_sequencing/results_per_pid/SEQC2_LL1/alignment/control01_SEQC2_LL1_merged.mdup.bam.bai |
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sample,tumor,tumor_index,control,control_index | ||
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H021-HVSG6L,/omics/odcf/analysis/evaluation_projects/workflow-validation/sequencing_full_test/exon_sequencing/results_per_pid/V_H021-HVSG6L/alignment/tumor_V_H021-HVSG6L_merged.mdup.bam,/omics/odcf/analysis/evaluation_projects/workflow-validation/sequencing_full_test/exon_sequencing/results_per_pid/V_H021-HVSG6L/alignment/tumor_V_H021-HVSG6L_merged.mdup.bam.bai,/omics/odcf/analysis/evaluation_projects/workflow-validation/sequencing_full_test/exon_sequencing/results_per_pid/V_H021-HVSG6L/alignment/blood_V_H021-HVSG6L_merged.mdup.bam,/omics/odcf/analysis/evaluation_projects/workflow-validation/sequencing_full_test/exon_sequencing/results_per_pid/V_H021-HVSG6L/alignment/blood_V_H021-HVSG6L_merged.mdup.bam.bai |
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sample,tumor,tumor_index,control,control_index | ||
H021-182ECT,/omics/odcf/analysis/evaluation_projects/workflow-validation/sequencing_full_test/whole_genome_sequencing/results_per_pid/V_H021-182ECT/alignment/metastasis_V_H021-182ECT_merged.mdup.bam,/omics/odcf/analysis/evaluation_projects/workflow-validation/sequencing_full_test/whole_genome_sequencing/results_per_pid/V_H021-182ECT/alignment/metastasis_V_H021-182ECT_merged.mdup.bam.bai,/omics/odcf/analysis/evaluation_projects/workflow-validation/sequencing_full_test/whole_genome_sequencing/results_per_pid/V_H021-182ECT/alignment/buffy_coat02_V_H021-182ECT_merged.mdup.bam,/omics/odcf/analysis/evaluation_projects/workflow-validation/sequencing_full_test/whole_genome_sequencing/results_per_pid/V_H021-182ECT/alignment/buffy_coat02_V_H021-182ECT_merged.mdup.bam.bai | ||
K26K-EVVHM1,/omics/odcf/analysis/evaluation_projects/workflow-validation/sequencing_full_test/whole_genome_sequencing/results_per_pid/V_K26K-EVVHM1/alignment/metastasis12_V_K26K-EVVHM1_merged.mdup.bam,/omics/odcf/analysis/evaluation_projects/workflow-validation/sequencing_full_test/whole_genome_sequencing/results_per_pid/V_K26K-EVVHM1/alignment/metastasis12_V_K26K-EVVHM1_merged.mdup.bam.bai,/omics/odcf/analysis/evaluation_projects/workflow-validation/sequencing_full_test/whole_genome_sequencing/results_per_pid/V_K26K-EVVHM1/alignment/buffy_coat1_V_K26K-EVVHM1_merged.mdup.bam,/omics/odcf/analysis/evaluation_projects/workflow-validation/sequencing_full_test/whole_genome_sequencing/results_per_pid/V_K26K-EVVHM1/alignment/buffy_coat1_V_K26K-EVVHM1_merged.mdup.bam.bai | ||
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