diff --git a/Changes b/Changes index c94a0c773..89021269e 100644 --- a/Changes +++ b/Changes @@ -1,6 +1,9 @@ CHANGES LOG ----------- +release 0.16.1 + - add tempdir parameter and verbose (-v) flag for teepot + release 0.16 - human split: new alignment_wtsi_stage2_humansplit_template.json, seqchksum_hs.json; addition of subst_params to alignment_common - seqchksum comparisons: merge bamseqchksum files for outputs for comparison with initial bam file in seqchksum.json diff --git a/data/vtlib/alignment_common.json b/data/vtlib/alignment_common.json index 977a96ae3..345addb38 100644 --- a/data/vtlib/alignment_common.json +++ b/data/vtlib/alignment_common.json @@ -85,6 +85,17 @@ ], "postproc":{"op":"concat", "pad":""} } + }, + {"id":"teepot_tempdir_value","required":"no","default":"."}, + { + "id":"teepot_tempdir_flag", + "required":"no", + "subst_constructor":{ + "vals":[ + "-t", + {"subst":"teepot_tempdir_value"} + ] + } } ] } diff --git a/data/vtlib/alignment_wtsi_stage2_humansplit_template.json b/data/vtlib/alignment_wtsi_stage2_humansplit_template.json index 7894ddeec..17018ea42 100644 --- a/data/vtlib/alignment_wtsi_stage2_humansplit_template.json +++ b/data/vtlib/alignment_wtsi_stage2_humansplit_template.json @@ -253,8 +253,8 @@ "type":"EXEC", "use_STDIN": true, "use_STDOUT": false, - "comment":"large wait (500 minutes) to avoid unnecessary spill to disk", - "cmd":["teepot", "-w", "30000", "-m", "1G", "__PHIX_ALN_OUT__", "__TGT_ALN_OUT__", "__HUMAN_SPLIT_OUT__" ] + "comment":"large wait (500 minutes) to avoid unnecessary spill to disk; specify parameter value teepot_tempdir_value to specify teepot tempdir", + "cmd":["teepot", "-v", {"subst":"teepot_tempdir_flag"}, "-w", "30000", "-m", "1G", "__PHIX_ALN_OUT__", "__TGT_ALN_OUT__", "__HUMAN_SPLIT_OUT__" ] }, { "id":"pre_alignment_target", @@ -353,8 +353,8 @@ "orig_type":"EXEC", "orig_use_STDIN": true, "orig_use_STDOUT": false, - "orig_comment":"large wait (500 minutes) to avoid unnecessary spill to disk - temporarily reduced to 166.6 mins", - "orig_cmd":["teepot", "-vv", "-w", "30000", "-m", "1G", "__TGT_OUT__", "__HUMAN_SPLIT_OUT__" ] + "orig_comment":"large wait (500 minutes) to avoid unnecessary spill to disk; specify parameter value teepot_tempdir_value to specify teepot tempdir", + "orig_cmd":["teepot", {"subst":"teepot_tempdir_flag"}, "-vv", "-w", "30000", "-m", "1G", "__TGT_OUT__", "__HUMAN_SPLIT_OUT__" ] }, { "id":"alignment_filter", diff --git a/data/vtlib/alignment_wtsi_stage2_template.json b/data/vtlib/alignment_wtsi_stage2_template.json index d3bb19b9b..81c2ee2f5 100644 --- a/data/vtlib/alignment_wtsi_stage2_template.json +++ b/data/vtlib/alignment_wtsi_stage2_template.json @@ -189,8 +189,8 @@ "type":"EXEC", "use_STDIN": true, "use_STDOUT": false, - "comment":"large wait (500 minutes) to avoid unnecessary spill to disk", - "cmd":["teepot", "-w", "30000", "-m", "1G", "__PHIX_ALN_OUT__", "__TGT_ALN_OUT__" ] + "comment":"large wait (500 minutes) to avoid unnecessary spill to disk; specify parameter value teepot_tempdir_value to specify teepot tempdir", + "cmd":["teepot", "-v", {"subst":"teepot_tempdir_flag"}, "-w", "30000", "-m", "1G", "__PHIX_ALN_OUT__", "__TGT_ALN_OUT__" ] }, { "id":"pre_alignment_target", diff --git a/data/vtlib/final_output_prep.json b/data/vtlib/final_output_prep.json index f557403e7..18cdda78d 100644 --- a/data/vtlib/final_output_prep.json +++ b/data/vtlib/final_output_prep.json @@ -427,7 +427,8 @@ "type":"EXEC", "use_STDIN": true, "use_STDOUT": false, - "cmd":["teepot", "-w", "300", "__SCRAMBLE_OUT__", "__BAMCHECK_OUT__", "__FLAGSTAT_OUT__", "__CALIBRATION_PU_OUT__", "__BAM_OUT__", "__SAMTOOLS_STATS_F0x900__", "__SAMTOOLS_STATS_F0xB00__", "__SEQCHKSUM_OUT__", "__SEQCHKSUM_EXTRAHASH_OUT__" ] + "comment":"specify parameter value teepot_tempdir_value to specify teepot tempdir", + "cmd":["teepot", "-v", {"subst":"teepot_tempdir_flag"}, "-w", "300", "__SCRAMBLE_OUT__", "__BAMCHECK_OUT__", "__FLAGSTAT_OUT__", "__CALIBRATION_PU_OUT__", "__BAM_OUT__", "__SAMTOOLS_STATS_F0x900__", "__SAMTOOLS_STATS_F0xB00__", "__SEQCHKSUM_OUT__", "__SEQCHKSUM_EXTRAHASH_OUT__" ] }, { "id":"scramble", @@ -441,8 +442,8 @@ "type":"EXEC", "use_STDIN": true, "use_STDOUT": false, - "cmd":["teepot", "-w", "30000", "__CRAM_OUT__", "__CRAI_OUT__", "__MD5_OUT__", "__SEQCHKSUM_OUT__" ], - "comment":"allow a generous 500 minutes for the teepot timeout" + "cmd":["teepot", "-v", {"subst":"teepot_tempdir_flag"}, "-w", "30000", "__CRAM_OUT__", "__CRAI_OUT__", "__MD5_OUT__", "__SEQCHKSUM_OUT__" ], + "comment":"allow a generous 500 minutes for the teepot timeout;specify parameter value teepot_tempdir_value to specify teepot tempdir" }, { "id":"scramble_md5", diff --git a/data/vtlib/post_alignment.json b/data/vtlib/post_alignment.json index ab6daeece..fa24d2a6d 100644 --- a/data/vtlib/post_alignment.json +++ b/data/vtlib/post_alignment.json @@ -52,8 +52,8 @@ "type":"EXEC", "use_STDIN": true, "use_STDOUT": false, - "cmd":["teepot", "-w", "300", "-m", "5M", "__HEADER_FIX_OUT__", "__FULL_BAM_OUT__"], - "comment":"get deadlock when tee used here" + "cmd":["teepot", "-v", {"subst":"teepot_tempdir_flag"}, "-w", "300", "-m", "5M", "__HEADER_FIX_OUT__", "__FULL_BAM_OUT__"], + "comment":"get deadlock when tee used here; specify parameter value teepot_tempdir_value to specify teepot tempdir" }, { "id":"sam_headerSQfix", @@ -76,7 +76,7 @@ "type":"EXEC", "use_STDIN": true, "use_STDOUT": true, - "cmd":["teepot", "-m", "5M", "-"] + "cmd":["teepot", "-v", "-m", "5M", "-"] }, { "id":"reheader_headerSQfix", diff --git a/data/vtlib/realignment_wtsi_template.json b/data/vtlib/realignment_wtsi_template.json index 08d05ddf2..df92b3e9f 100644 --- a/data/vtlib/realignment_wtsi_template.json +++ b/data/vtlib/realignment_wtsi_template.json @@ -194,7 +194,8 @@ "type":"EXEC", "use_STDIN": true, "use_STDOUT": false, - "cmd":["teepot", "__PHIX_ALN_OUT__", "__TGT_ALN_OUT__"] + "cmd":["teepot", "-v", {"subst":"teepot_tempdir_flag"}, "__PHIX_ALN_OUT__", "__TGT_ALN_OUT__"], + "comment":"specify parameter value teepot_tempdir_value to specif teepot tempdir" }, { "id":"pre_alignment_target",