From bf056182456ce024101a6271a3a8ce3f38bf20b8 Mon Sep 17 00:00:00 2001 From: Kevin Lewis Date: Thu, 9 Nov 2023 14:13:32 +0000 Subject: [PATCH] change final_output_prep template to produce crai files using "samtools index" rather than "cram_index" --- data/vtlib/final_output_prep.json | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/data/vtlib/final_output_prep.json b/data/vtlib/final_output_prep.json index c498464e..34420a99 100644 --- a/data/vtlib/final_output_prep.json +++ b/data/vtlib/final_output_prep.json @@ -368,7 +368,12 @@ "type":"EXEC", "use_STDIN": true, "use_STDOUT": false, - "cmd":[ "cram_index", "-", {"subst":"crai_file"} ] + "cmd": [ + {"subst":"samtools_executable", "required":true, "ifnull":"samtools"}, "index", + {"subst":"cram_index_extra_flags", "required":false}, + {"port":"cram", "direction":"in"}, + {"port":"idx", "direction":"out"} + ] }, { "id":"cram_seqchksum", @@ -517,7 +522,8 @@ } }, { "id":"cram_tee_to_md5", "from":"cram_tee:md5", "to":"create_cram_md5" }, - { "id":"cram_tee_to_crai", "from":"cram_tee:crai", "to":"cram_index" }, + { "id":"bam_to_idx", "from":"cram_tee:crai", "to":"cram_index:cram" }, + { "id":"idx_to_file", "from":"cram_index:idx", "to":"crai_file" }, { "id":"cram_tee_to_bscs", "from":"cram_tee:seqchksum", "to":"cram_seqchksum" }, { "id":"md5_to_postprocess", "from":"create_cram_md5", "to":"postprocess_md5" }, { "id":"bmdmw_to_sts_F0x900", "from":"bmd_multiway:samtools_stats_F0x900", "to":"samtools_stats_F0x900" },