Merge 232c0d0 into 02d19db

definitions/install_rd_rna_parameters.yaml

@@ -26,6 +26,7 @@ emip:
     numpy:
     picard: 2.18
     pip:
+    preseq: 2.0.3
     python: 2.7
     r-optparse:
     r-readr:
@@ -156,6 +157,9 @@ program_test_command:
   picard:
     execution:
     path: 'picard'
+  preseq:
+    execution: 'preseq'
+    path: 'preseq'
   r-optparse:
     execution: 'R -e "library(tximport)"'
     path:

definitions/rd_rna_initiation_map.yaml

@@ -1,33 +1,34 @@
+---
 CHAIN_ALL:
-   - CHAIN_MAIN:
-   - gzip_fastq
+  - CHAIN_MAIN:
+    - gzip_fastq
 # Parallel chains (branch)
-   - CHAIN_FASTQ:
-      - fastqc
-   - CHAIN_DE:
-      - salmon_quant
-      - blobfish
-   - CHAIN_FUSION:
-      - star_fusion
-   - CHAIN_MAIN:
-      - star_aln
-      - picardtools_mergesamfiles
-      - CHAIN_STRINGTIE:
-         - stringtie_ar
-         - gffcompare_ar
-   - CHAIN_MAIN:
-      - markduplicates
-      - CHAIN_RSEQC:
-         - PARALLEL:
-            - rseqc
-            - genebody_coverage
-   - CHAIN_MAIN:
-      - gatk_splitncigarreads
-      - gatk_baserecalibration
-      - gatk_haplotypecaller
-      - gatk_variantfiltration
-      - CHAIN_ASE:
-         - gatk_asereadcounter
-         - bootstrapann
-   - multiqc_ar
-   - sacct
+  - CHAIN_FASTQ:
+    - fastqc_ar
+  - CHAIN_DE:
+    - salmon_quant
+    - blobfish
+  - CHAIN_FUSION:
+    - star_fusion
+  - CHAIN_MAIN:
+    - star_aln
+    - picardtools_mergesamfiles
+    - CHAIN_STRINGTIE:
+      - stringtie_ar
+      - gffcompare_ar
+    - CHAIN_QC:
+      - PARALLEL:
+        - preseq_ar
+        - rseqc
+        - genebody_coverage
+  - CHAIN_MAIN:
+    - markduplicates
+    - gatk_splitncigarreads
+    - gatk_baserecalibration
+    - gatk_haplotypecaller
+    - gatk_variantfiltration
+    - CHAIN_ASE:
+      - gatk_asereadcounter
+      - bootstrapann
+  - multiqc_ar
+  - sacct