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Merge pull request #26 from ghga-de/fix-annotation-file-input
final annotation fix
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@@ -38,7 +38,6 @@ The pipeline has 6 main steps: Indel calling using platypus, basic annotations, | |
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Reliability and confidation annotations: It is an optional ste for mapability, hiseq, selfchain and repeat regions checks for reliability and confidence of those scores. | ||
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3. Deep Annotation (--runIndelDeepAnnotation True): | ||
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If basic annotations are applied, an extra optional step for number of extra indel annotations like enhancer, cosmic, mirBASE, encode databases can be applied too. | ||
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@@ -207,7 +206,6 @@ We thank the following people for their extensive assistance in the development | |
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- Nagarajan Paramasivam (@NagaComBio) [email protected] | ||
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**TODO** | ||
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<!-- TODO nf-core: If applicable, make list of people who have also contributed --> | ||
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@@ -1,3 +1,3 @@ | ||
#!/bin/bash | ||
module load nextflow/22.07.1-edge | ||
nextflow run main.nf -profile test,singularity --input testdata/samplesheet_test.csv | ||
nextflow run main.nf -profile dkfz_cluster_38,singularity --input testdata/samplesheet_test.csv -resume |
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@@ -1,2 +1,4 @@ | ||
sample,tumor,tumor_index,control,control_index | ||
test_withcontrol,testdata/WES_LL_T_1_test.bam,testdata/WES_LL_T_1_test.bam.bai,testdata/WES_LL_N_1_test.bam,testdata/WES_LL_N_1_test.bam.bai | ||
test,testdata/WES_LL_T_1_test.bam,testdata/WES_LL_T_1_test.bam.bai,testdata/WES_LL_N_1_test.bam,testdata/WES_LL_N_1_test.bam.bai | ||
test_2,testdata/WES_LL_T_1_test.bam,testdata/WES_LL_T_1_test.bam.bai,testdata/WES_LL_N_1_test.bam,testdata/WES_LL_N_1_test.bam.bai | ||
test_3,testdata/WES_LL_T_1_test.bam,testdata/WES_LL_T_1_test.bam.bai,testdata/WES_LL_N_1_test.bam,testdata/WES_LL_N_1_test.bam.bai |
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