From bc7c7ed9a567ec8c7292be1c3730246adab3787a Mon Sep 17 00:00:00 2001 From: Steven Leonard Date: Thu, 19 Dec 2019 10:18:02 +0000 Subject: [PATCH 1/7] added BotSeq markduplicates method --- Changes | 2 ++ data/vtlib/final_output_prep.json | 3 ++- data/vtlib/markdup_botseq.json | 38 +++++++++++++++++++++++++++++++ 3 files changed, 42 insertions(+), 1 deletion(-) create mode 100644 data/vtlib/markdup_botseq.json diff --git a/Changes b/Changes index 3057c43ca..b40f388c0 100644 --- a/Changes +++ b/Changes @@ -1,6 +1,8 @@ CHANGES LOG ----------- + - add markdup_botseq.json + 0.26.0 - add parameters file for top-up merge - functional equivalence: enable selection of markdup method - biobambam (default), samtools or picard diff --git a/data/vtlib/final_output_prep.json b/data/vtlib/final_output_prep.json index 4c3301ad7..7705ef5b0 100644 --- a/data/vtlib/final_output_prep.json +++ b/data/vtlib/final_output_prep.json @@ -264,7 +264,8 @@ "cases":{ "samtools":"markdup_samtools.json", "picard":"markdup_picard.json", - "biobambam":"markdup_biobambam.json" + "biobambam":"markdup_biobambam.json", + "botseq":"markdup_botseq.json" } } }, diff --git a/data/vtlib/markdup_botseq.json b/data/vtlib/markdup_botseq.json new file mode 100644 index 000000000..ca63faed0 --- /dev/null +++ b/data/vtlib/markdup_botseq.json @@ -0,0 +1,38 @@ +{ +"version":"2.0", +"description":"steps in the alignment pipeline to post-process bam files produced by the AlignmentFilter", +"subgraph_io":{ + "ports":{ + "inputs":{ "_stdin_":"bamsort_coord" }, + "outputs":{ "_stdout_":"bammarkduplicates" } + } +}, +"nodes":[ + { + "id":"bamsort_coord_output", + "type":"RAFILE", + "name": "bamsort_coord.bam" + }, + { + "id":"bamsort_coord", + "type":"EXEC", + "use_STDIN": true, + "use_STDOUT": true, + "cmd": [ {"subst":"bsc_executable", "required":"yes", "ifnull":"bamsormadup"}, {"subst":"bsmd_threads"}, "SO=coordinate", "verbose=0", "fixmate=1", "rcsupport=1", {"subst":"bs_tmpfile_flag"} ] + }, + { + "id":"bammarkduplicates", + "comment":"default tool bammarkduplicatesopt from Biobambam >= 2.0.65", + "type":"EXEC", + "use_STDIN": true, + "use_STDOUT": true, + "cmd": [ "bammarkduplicatesopt", "level=0", "verbose=0", {"subst":"bmd_tmpfile_flag"}, {"subst":"bmd_metrics_file_flag"}, + {"subst":"optical_distance_flag","ifnull":{"subst_constructor":{"vals":[ "optminpixeldif", {"subst":"markdup_optical_distance_value","required":false,"ifnull":2500} ], "postproc":{"op":"concat","pad":"="}}}} ] + } +], +"edges":[ + + { "id":"coordsort_todisk", "from":"bamsort_coord", "to":"bamsort_coord_output" }, + { "id":"disk_tomarkdup", "from":"bamsort_coord_output", "to":"bammarkduplicates" } +] +} From 8d3268c753b5e00bec514a371197ae96fa6c0276 Mon Sep 17 00:00:00 2001 From: Your Name Date: Thu, 27 Feb 2020 14:01:17 +0000 Subject: [PATCH 2/7] renamed markdup_botseq.json markdup_duplexseq.json --- Changes | 1 + 1 file changed, 1 insertion(+) diff --git a/Changes b/Changes index b40f388c0..4dc42d16b 100644 --- a/Changes +++ b/Changes @@ -1,6 +1,7 @@ CHANGES LOG ----------- + - renamed markdup_botseq.json markdup_duplexseq.json - add markdup_botseq.json 0.26.0 From c43cf743edc5e348ca0c1837e13be7ea7126bb00 Mon Sep 17 00:00:00 2001 From: Your Name Date: Fri, 28 Feb 2020 09:23:07 +0000 Subject: [PATCH 3/7] explictly commit renamed file --- data/vtlib/markdup_duplexseq.json | 38 +++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 data/vtlib/markdup_duplexseq.json diff --git a/data/vtlib/markdup_duplexseq.json b/data/vtlib/markdup_duplexseq.json new file mode 100644 index 000000000..ca63faed0 --- /dev/null +++ b/data/vtlib/markdup_duplexseq.json @@ -0,0 +1,38 @@ +{ +"version":"2.0", +"description":"steps in the alignment pipeline to post-process bam files produced by the AlignmentFilter", +"subgraph_io":{ + "ports":{ + "inputs":{ "_stdin_":"bamsort_coord" }, + "outputs":{ "_stdout_":"bammarkduplicates" } + } +}, +"nodes":[ + { + "id":"bamsort_coord_output", + "type":"RAFILE", + "name": "bamsort_coord.bam" + }, + { + "id":"bamsort_coord", + "type":"EXEC", + "use_STDIN": true, + "use_STDOUT": true, + "cmd": [ {"subst":"bsc_executable", "required":"yes", "ifnull":"bamsormadup"}, {"subst":"bsmd_threads"}, "SO=coordinate", "verbose=0", "fixmate=1", "rcsupport=1", {"subst":"bs_tmpfile_flag"} ] + }, + { + "id":"bammarkduplicates", + "comment":"default tool bammarkduplicatesopt from Biobambam >= 2.0.65", + "type":"EXEC", + "use_STDIN": true, + "use_STDOUT": true, + "cmd": [ "bammarkduplicatesopt", "level=0", "verbose=0", {"subst":"bmd_tmpfile_flag"}, {"subst":"bmd_metrics_file_flag"}, + {"subst":"optical_distance_flag","ifnull":{"subst_constructor":{"vals":[ "optminpixeldif", {"subst":"markdup_optical_distance_value","required":false,"ifnull":2500} ], "postproc":{"op":"concat","pad":"="}}}} ] + } +], +"edges":[ + + { "id":"coordsort_todisk", "from":"bamsort_coord", "to":"bamsort_coord_output" }, + { "id":"disk_tomarkdup", "from":"bamsort_coord_output", "to":"bammarkduplicates" } +] +} From 053092fb9e6d18b1c9e8910069e4011ac8820775 Mon Sep 17 00:00:00 2001 From: Your Name Date: Fri, 28 Feb 2020 11:17:41 +0000 Subject: [PATCH 4/7] updated markdup_method list to reflect change from botseq to duplexseq --- data/vtlib/final_output_prep.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/data/vtlib/final_output_prep.json b/data/vtlib/final_output_prep.json index 7705ef5b0..d20600bf8 100644 --- a/data/vtlib/final_output_prep.json +++ b/data/vtlib/final_output_prep.json @@ -265,7 +265,7 @@ "samtools":"markdup_samtools.json", "picard":"markdup_picard.json", "biobambam":"markdup_biobambam.json", - "botseq":"markdup_botseq.json" + "duplexseq":"markdup_duplexseq.json" } } }, From e9f5096bb59376b2f0f8debdb72b3165a086b26a Mon Sep 17 00:00:00 2001 From: Your Name Date: Fri, 28 Feb 2020 11:20:03 +0000 Subject: [PATCH 5/7] renamed markdup_botseq.json markdup_duplexseq.json --- data/vtlib/markdup_botseq.json | 38 ---------------------------------- 1 file changed, 38 deletions(-) delete mode 100644 data/vtlib/markdup_botseq.json diff --git a/data/vtlib/markdup_botseq.json b/data/vtlib/markdup_botseq.json deleted file mode 100644 index ca63faed0..000000000 --- a/data/vtlib/markdup_botseq.json +++ /dev/null @@ -1,38 +0,0 @@ -{ -"version":"2.0", -"description":"steps in the alignment pipeline to post-process bam files produced by the AlignmentFilter", -"subgraph_io":{ - "ports":{ - "inputs":{ "_stdin_":"bamsort_coord" }, - "outputs":{ "_stdout_":"bammarkduplicates" } - } -}, -"nodes":[ - { - "id":"bamsort_coord_output", - "type":"RAFILE", - "name": "bamsort_coord.bam" - }, - { - "id":"bamsort_coord", - "type":"EXEC", - "use_STDIN": true, - "use_STDOUT": true, - "cmd": [ {"subst":"bsc_executable", "required":"yes", "ifnull":"bamsormadup"}, {"subst":"bsmd_threads"}, "SO=coordinate", "verbose=0", "fixmate=1", "rcsupport=1", {"subst":"bs_tmpfile_flag"} ] - }, - { - "id":"bammarkduplicates", - "comment":"default tool bammarkduplicatesopt from Biobambam >= 2.0.65", - "type":"EXEC", - "use_STDIN": true, - "use_STDOUT": true, - "cmd": [ "bammarkduplicatesopt", "level=0", "verbose=0", {"subst":"bmd_tmpfile_flag"}, {"subst":"bmd_metrics_file_flag"}, - {"subst":"optical_distance_flag","ifnull":{"subst_constructor":{"vals":[ "optminpixeldif", {"subst":"markdup_optical_distance_value","required":false,"ifnull":2500} ], "postproc":{"op":"concat","pad":"="}}}} ] - } -], -"edges":[ - - { "id":"coordsort_todisk", "from":"bamsort_coord", "to":"bamsort_coord_output" }, - { "id":"disk_tomarkdup", "from":"bamsort_coord_output", "to":"bammarkduplicates" } -] -} From c72b8c2632721271cb48fd5c6b2bc2282042f4de Mon Sep 17 00:00:00 2001 From: Steven Leonard Date: Wed, 25 Nov 2020 11:15:13 +0000 Subject: [PATCH 6/7] added markdup files --- MANIFEST | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/MANIFEST b/MANIFEST index 53389cfb0..5f35cf90f 100644 --- a/MANIFEST +++ b/MANIFEST @@ -33,6 +33,10 @@ data/vtlib/seqchksum_realign.json data/vtlib/split_by_chromosome.json data/vtlib/star_alignment.json data/vtlib/tophat2_alignment.json +data/vtlib/markdup_biobambam.json +data/vtlib/markdup_duplexseq.json +data/vtlib/markdup_picard.json +data/vtlib/markdup_samtools.json examples/bwa_aln_cfg.png examples/bwa_mem/bwa_mem_alignment.vtf examples/bwa_mem/generic_alignment_with_phix.vtf From e59cd8d30d6a4deada190d9791aa1b5a8dc02506 Mon Sep 17 00:00:00 2001 From: Kevin Lewis Date: Wed, 25 Nov 2020 14:57:42 +0000 Subject: [PATCH 7/7] Update final_output_prep.json add missing comma --- data/vtlib/final_output_prep.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/data/vtlib/final_output_prep.json b/data/vtlib/final_output_prep.json index 9e2681327..a65aeca60 100644 --- a/data/vtlib/final_output_prep.json +++ b/data/vtlib/final_output_prep.json @@ -265,7 +265,7 @@ "samtools":"markdup_samtools.json", "picard":"markdup_picard.json", "biobambam":"markdup_biobambam.json", - "duplexseq":"markdup_duplexseq.json" + "duplexseq":"markdup_duplexseq.json", "none":"markdup_none.json" } }