diff --git a/data/vtlib/alignment_wtsi_stage2_humansplit_extrasplit_notargetalign_template.json b/data/vtlib/alignment_wtsi_stage2_humansplit_extrasplit_notargetalign_template.json index 09a8e4551..67660efe1 100644 --- a/data/vtlib/alignment_wtsi_stage2_humansplit_extrasplit_notargetalign_template.json +++ b/data/vtlib/alignment_wtsi_stage2_humansplit_extrasplit_notargetalign_template.json @@ -384,7 +384,6 @@ { "id":"final_output_prep_target", "type":"VTFILE", - "old_comment":"inputs: _stdin_ (bam), reference_genome_fasta (for scramble); outputs: _stdout_ (bam)", "comment":"inputs: _stdin_ (bam); outputs: _stdout_ (bam)", "node_prefix":"foptgt_", "subst_map":{"phix_or_target":{"subst":"target_indicator"},"fopid":{"subst":"fopid_tgt"},"bstmp":"bsfopt","brtmp":"brfopt","bmdtmp":"bmdfopt"}, @@ -394,7 +393,6 @@ { "id":"final_output_prep_phix", "type":"VTFILE", - "old_comment":"inputs: _stdin_ (bam), reference_genome_fasta (for scramble); outputs: _stdout_ (bam)", "comment":"inputs: _stdin_ (bam); outputs: _stdout_ (bam)", "node_prefix":"fopphx_", "subst_map":{"phix_or_target":{"subst":"phix_indicator"},"fopid":{"subst":"fopid_phix"},"bstmp":"bsfopp","brtmp":"brfopp","bmdtmp":"bmdfopp","scramble_reference_fasta":{"subst":"phix_reference_genome_fasta"}}, @@ -404,7 +402,6 @@ { "id":"final_output_prep_es", "type":"VTFILE", - "old_comment":"inputs: _stdin_ (bam), reference_genome_fasta (for scramble); outputs: _stdout_ (bam)", "comment":"inputs: _stdin_ (bam); outputs: _stdout_ (bam)", "node_prefix":"fopes_", "subst_map":{"phix_or_target":{"subst":"es_indicator"},"fopid":{"subst":"fopid_es"},"bstmp":"bsfoph","brtmp":"brfoph","bmdtmp":"bmdfoph","scramble_reference_fasta":{"subst":"es_reference_genome_fasta"}}, @@ -414,7 +411,6 @@ { "id":"final_output_prep_hs", "type":"VTFILE", - "old_comment":"inputs: _stdin_ (bam), reference_genome_fasta (for scramble); outputs: _stdout_ (bam)", "comment":"inputs: _stdin_ (bam); outputs: _stdout_ (bam)", "node_prefix":"fophs_", "subst_map":{"phix_or_target":{"subst":"hs_indicator"},"fopid":{"subst":"fopid_hs"},"bstmp":"bsfoph","brtmp":"brfoph","bmdtmp":"bmdfoph","scramble_reference_fasta":{"subst":"hs_reference_genome_fasta"}}, diff --git a/data/vtlib/alignment_wtsi_stage2_humansplit_notargetalign_template.json b/data/vtlib/alignment_wtsi_stage2_humansplit_notargetalign_template.json index e450bb50c..1f60d0671 100644 --- a/data/vtlib/alignment_wtsi_stage2_humansplit_notargetalign_template.json +++ b/data/vtlib/alignment_wtsi_stage2_humansplit_notargetalign_template.json @@ -288,7 +288,6 @@ { "id":"final_output_prep_target", "type":"VTFILE", - "old_comment":"inputs: _stdin_ (bam), reference_genome_fasta (for scramble); outputs: _stdout_ (bam)", "comment":"inputs: _stdin_ (bam); outputs: _stdout_ (bam)", "node_prefix":"foptgt_", "subst_map":{"phix_or_target":{"subst":"target_indicator"},"fopid":{"subst":"fopid_tgt"},"bstmp":"bsfopt","brtmp":"brfopt","bmdtmp":"bmdfopt"}, @@ -298,7 +297,6 @@ { "id":"final_output_prep_phix", "type":"VTFILE", - "old_comment":"inputs: _stdin_ (bam), reference_genome_fasta (for scramble); outputs: _stdout_ (bam)", "comment":"inputs: _stdin_ (bam); outputs: _stdout_ (bam)", "node_prefix":"fopphx_", "subst_map":{"phix_or_target":{"subst":"phix_indicator"},"fopid":{"subst":"fopid_phix"},"bstmp":"bsfopp","brtmp":"brfopp","bmdtmp":"bmdfopp","scramble_reference_fasta":{"subst":"phix_reference_genome_fasta"}}, @@ -308,7 +306,6 @@ { "id":"final_output_prep_hs", "type":"VTFILE", - "old_comment":"inputs: _stdin_ (bam), reference_genome_fasta (for scramble); outputs: _stdout_ (bam)", "comment":"inputs: _stdin_ (bam); outputs: _stdout_ (bam)", "node_prefix":"fophs_", "subst_map":{"phix_or_target":{"subst":"hs_indicator"},"fopid":{"subst":"fopid_hs"},"bstmp":"bsfoph","brtmp":"brfoph","bmdtmp":"bmdfoph","scramble_reference_fasta":{"subst":"hs_reference_genome_fasta"}}, diff --git a/data/vtlib/bcl2bam_phix_deplex_wtsi_stage1_template.json b/data/vtlib/bcl2bam_phix_deplex_wtsi_stage1_template.json index dd2aeef3c..754361b03 100644 --- a/data/vtlib/bcl2bam_phix_deplex_wtsi_stage1_template.json +++ b/data/vtlib/bcl2bam_phix_deplex_wtsi_stage1_template.json @@ -310,7 +310,11 @@ "use_STDOUT": true, "cmd": {"select":"s1_output_format", "default":"cram", "select_range":[1], "cases":{ "bam":[ "bamrecompress", "verbose=0", "md5=1", {"subst":"br_md5file_flag","required":"yes","ifnull":{"subst_constructor":{"vals":[ "md5filename", {"subst":"md5filename"} ],"postproc":{"op":"concat","pad":"="}}}}, {"subst":"br_numthreads_flag", "ifnull":{"subst_constructor":{"vals":[ "numthreads", {"subst":"br_numthreads_val","ifnull":{"subst":"aligner_numthreads"}} ],"postproc":{"op":"concat", "pad":"="}}}} ], - "cram":["scramble", "-x", "-I", "bam", "-O", "cram"] + "cram": [ + {"subst":"samtools_executable"}, "view", "-C", + "--output-fmt-option", "no_ref", + "-" + ] }} }, { diff --git a/data/vtlib/bwa_aln_alignment.json b/data/vtlib/bwa_aln_alignment.json index f2c88f285..035e0b879 100644 --- a/data/vtlib/bwa_aln_alignment.json +++ b/data/vtlib/bwa_aln_alignment.json @@ -81,11 +81,10 @@ "use_STDIN":true, "use_STDOUT":true, "cmd":[ - "scramble", - {"subst":"s2b_compress_level", "ifnull":"-0"}, - {"subst":"s2b_mt", "ifnull":{"subst_constructor":{ "vals":[ "-t", {"subst":"s2b_mt_val"} ]}}}, - "-I", "sam", - "-O", "bam" + {"subst":"samtools_executable"}, "view", "-b", + {"subst_constructor":{"vals":[ "--output-fmt-option", {"subst_constructor":{"vals":[ "level", {"subst":"s2b_compression_level","ifnull":0} ], "postproc":{"op":"concat", "pad":"="}}}]}}, + {"subst_constructor":{"vals":[ "--threads", {"subst":"s2b_threads","ifnull":{"subst":"s2b_mt_val"}}]}}, + "-" ] } ], @@ -98,6 +97,6 @@ { "id":"cat1_to_sampe2", "from":"simple_cat2", "to":"bwa_sampe:bam_2" }, { "id":"aln1_sai_to_sampe", "from":"bwa_aln_1", "to":"bwa_sampe:sai_1" }, { "id":"aln2_sai_to_sampe", "from":"bwa_aln_2", "to":"bwa_sampe:sai_2" }, - { "id":"bwa_sampe_to_scramble", "from":"bwa_sampe", "to":"samtobam" } + { "id":"bwa_sampe_to_s2b", "from":"bwa_sampe", "to":"samtobam" } ] } diff --git a/data/vtlib/bwa_aln_se_alignment.json b/data/vtlib/bwa_aln_se_alignment.json index 747fce0ea..f891da8fd 100644 --- a/data/vtlib/bwa_aln_se_alignment.json +++ b/data/vtlib/bwa_aln_se_alignment.json @@ -64,11 +64,10 @@ "use_STDIN":true, "use_STDOUT":true, "cmd":[ - "scramble", - {"subst":"s2b_mt", "ifnull":{"subst_constructor":{ "vals":[ "-t", {"subst":"s2b_mt_val"} ]}}}, - {"subst":"s2b_compress_level", "ifnull":"-0"}, - "-I", "sam", - "-O", "bam" + {"subst":"samtools_executable"}, "view", "-b", + {"subst_constructor":{"vals":[ "--threads", {"subst":"s2b_threads","ifnull":{"subst":"s2b_mt_val"}}]}}, + {"subst_constructor":{"vals":[ "--output-fmt-option", {"subst_constructor":{"vals":[ "level", {"subst":"s2b_compression_level","ifnull":0} ], "postproc":{"op":"concat", "pad":"="}}}]}}, + "-" ] } ], @@ -77,6 +76,6 @@ { "id":"tee_to_cat", "from":"tee2:sampe", "to":"simple_cat" }, { "id":"cat1_to_sampe", "from":"simple_cat", "to":"bwa_samse:bam" }, { "id":"aln_sai_to_samse", "from":"bwa_aln", "to":"bwa_samse:sai" }, - { "id":"bwa_samse_to_scramble", "from":"bwa_samse", "to":"samtobam" } + { "id":"bwa_samse_to_s2b", "from":"bwa_samse", "to":"samtobam" } ] } diff --git a/data/vtlib/bwa_mem_alignment.json b/data/vtlib/bwa_mem_alignment.json index 781727ea8..f14ae93c2 100644 --- a/data/vtlib/bwa_mem_alignment.json +++ b/data/vtlib/bwa_mem_alignment.json @@ -77,16 +77,15 @@ "use_STDIN":true, "use_STDOUT":true, "cmd":[ - "scramble", - {"subst":"s2b_mt", "ifnull":{"subst_constructor":{ "vals":[ "-t", {"subst":"s2b_mt_val"} ]}}}, - {"subst":"s2b_compress_level", "ifnull":"-0"}, - "-I", "sam", - "-O", "bam" + {"subst":"samtools_executable"}, "view", "-b", + {"subst_constructor":{"vals":[ "--threads", {"subst":"s2b_threads","ifnull":{"subst":"s2b_mt_val"}}]}}, + {"subst_constructor":{"vals":[ "--output-fmt-option", {"subst_constructor":{"vals":[ "level", {"subst":"s2b_compression_level","ifnull":0} ], "postproc":{"op":"concat", "pad":"="}}}]}}, + "-" ] } ], "edges":[ { "id":"bamtofastq_to_int_fq", "from":"bamtofastq", "to":"bwa_mem:fq" }, - { "id":"bwa_mem_to_scramble", "from":"bwa_mem", "to":"samtobam" } + { "id":"bwa_mem_to_s2b", "from":"bwa_mem", "to":"samtobam" } ] } diff --git a/data/vtlib/bwa_mem_bwakit_alignment.json b/data/vtlib/bwa_mem_bwakit_alignment.json index 5eb33874a..18c3aa970 100644 --- a/data/vtlib/bwa_mem_bwakit_alignment.json +++ b/data/vtlib/bwa_mem_bwakit_alignment.json @@ -78,17 +78,16 @@ "use_STDIN":true, "use_STDOUT":true, "cmd":[ - "scramble", - {"subst":"s2b_mt", "ifnull":{"subst_constructor":{ "vals":[ "-t", {"subst":"s2b_mt_val"} ]}}}, - {"subst":"s2b_compress_level", "ifnull":"-0"}, - "-I", "sam", - "-O", "bam" + {"subst":"samtools_executable"}, "view", "-b", + {"subst_constructor":{"vals":[ "--threads", {"subst":"s2b_threads","ifnull":{"subst":"s2b_mt_val"}}]}}, + {"subst_constructor":{"vals":[ "--output-fmt-option", {"subst_constructor":{"vals":[ "level", {"subst":"s2b_compression_level","ifnull":0} ], "postproc":{"op":"concat", "pad":"="}}}]}}, + "-" ] } ], "edges":[ { "id":"bamtofastq_to_int_fq", "from":"bamtofastq", "to":"bwa_mem:fq" }, { "id":"bwa_mem_to_bwa_postalt", "from":"bwa_mem", "to":"bwa-postalt" }, - { "id":"bwa_postalt_to_scramble", "from":"bwa-postalt", "to":"samtobam" } + { "id":"bwa_postalt_to_s2b", "from":"bwa-postalt", "to":"samtobam" } ] } diff --git a/data/vtlib/final_output_noalign_prep.json b/data/vtlib/final_output_noalign_prep.json index fa3060e4a..62f4a453d 100644 --- a/data/vtlib/final_output_noalign_prep.json +++ b/data/vtlib/final_output_noalign_prep.json @@ -144,24 +144,22 @@ "use_STDIN": true, "use_STDOUT": false, "comment":"specify parameter value teepot_tempdir_value to specify teepot tempdir", - "cmd":[ "teepot", {"subst":"teepot_vflag", "ifnull":"-v"}, {"subst":"teepot_tempdir_flag"}, "-w", {"subst":"fomw_teepot_wval", "ifnull":"7200"}, "__SCRAMBLE_OUT__", "__BAM_STATS_OUT__", "__FLAGSTAT_OUT__", "__BAM_OUT__", "__SAMTOOLS_STATS_F0x900_OUT__", "__SAMTOOLS_STATS_F0xB00_OUT__", "__SEQCHKSUM_OUT__", "__SEQCHKSUM_EXTRAHASH_OUT__" ] + "cmd":[ "teepot", {"subst":"teepot_vflag", "ifnull":"-v"}, {"subst":"teepot_tempdir_flag"}, "-w", {"subst":"fomw_teepot_wval", "ifnull":"7200"}, "__B2C_OUT__", "__BAM_STATS_OUT__", "__FLAGSTAT_OUT__", "__BAM_OUT__", "__SAMTOOLS_STATS_F0x900_OUT__", "__SAMTOOLS_STATS_F0xB00_OUT__", "__SEQCHKSUM_OUT__", "__SEQCHKSUM_EXTRAHASH_OUT__" ] }, { - "id":"scramble", + "id":"bam2cram", "type":"EXEC", "use_STDIN": true, "use_STDOUT": true, "cmd":[ - "scramble", - {"subst":"b2c_mt", "ifnull":{"subst_constructor":{ "vals":[ "-t", {"subst":"b2c_mt_val"} ]}}}, - {"subst":"b2c_fmtver", "ifnull":{"subst_constructor":{ "vals":[ "-V", {"subst":"b2c_format_version"} ]}}}, - {"subst":"b2c_compress_level", "ifnull":"-7"}, - "-I", "bam", - "-O", "cram" + {"subst":"samtools_executable"}, "view", "-C", + {"subst_constructor":{"vals":[ "--threads", {"subst":"b2c_threads","ifnull":{"subst":"b2c_mt_val"}}]}}, + {"subst_constructor":{"vals":[ "--output-fmt-option", {"subst_constructor":{"vals":[ "level", {"subst":"b2c_compression_level","ifnull":7} ], "postproc":{"op":"concat", "pad":"="}}}]}}, + "-" ] }, { - "id":"scramble_tee", + "id":"cram_tee", "type":"EXEC", "use_STDIN": true, "use_STDOUT": false, @@ -169,7 +167,7 @@ "comment":"allow a generous 500 minutes for the teepot timeout; specify parameter value teepot_tempdir_value to specify teepot tempdir" }, { - "id":"scramble_md5", + "id":"create_cram_md5", "type":"EXEC", "use_STDIN": true, "use_STDOUT": true, @@ -268,11 +266,11 @@ } ], "edges":[ - { "id":"bmdmw_to_scramble", "from":"fo_in_multiway:__SCRAMBLE_OUT__", "to":"scramble" }, - { "id":"scramble_to_scramble_tee", "from":"scramble", "to":"scramble_tee" }, - { "id":"scramble_tee_to_md5", "from":"scramble_tee:__MD5_OUT__", "to":"scramble_md5" }, - { "id":"scramble_tee_to_bscs", "from":"scramble_tee:__SEQCHKSUM_OUT__", "to":"cram_seqchksum" }, - { "id":"md5_to_postprocess", "from":"scramble_md5", "to":"postprocess_md5" }, + { "id":"bmdmw_to_b2c", "from":"fo_in_multiway:__B2C_OUT__", "to":"bam2cram" }, + { "id":"b2c_to_cram_tee", "from":"bam2cram", "to":"cram_tee" }, + { "id":"cram_tee_to_md5", "from":"cram_tee:__MD5_OUT__", "to":"create_cram_md5" }, + { "id":"cram_tee_to_bscs", "from":"cram_tee:__SEQCHKSUM_OUT__", "to":"cram_seqchksum" }, + { "id":"md5_to_postprocess", "from":"create_cram_md5", "to":"postprocess_md5" }, { "id":"bmdmw_to_sts_F0x900", "from":"fo_in_multiway:__SAMTOOLS_STATS_F0x900_OUT__", "to":"samtools_stats_F0x900" }, { "id":"bmdmw_to_sts_F0xB00", "from":"fo_in_multiway:__SAMTOOLS_STATS_F0xB00_OUT__", "to":"samtools_stats_F0xB00" }, { "id":"bmdmw_to_bam_stats", "from":"fo_in_multiway:__BAM_STATS_OUT__", "to":"bam_stats" }, @@ -282,7 +280,7 @@ { "id":"flagstat_filter_to_flagstat", "from":"flagstat_filter", "to":"flagstat" }, { "id":"bmd_to_bam", "from":"fo_in_multiway:__BAM_OUT__", "to":"bamrecompress" }, { "id":"brc_to_bam", "from":"bamrecompress", "to":"bam_file" }, - { "id":"tee_to_cram", "from":"scramble_tee:__CRAM_OUT__", "to":"cram_file" }, + { "id":"tee_to_cram", "from":"cram_tee:__CRAM_OUT__", "to":"cram_file" }, { "id":"corrected_md5_out", "from":"postprocess_md5", "to":"cram_md5" }, { "id":"scs_to_tee", "from":"seqchksum", "to":"seqchksum_tee" }, { "id":"scs_tee_to_file", "from":"seqchksum_tee:__FILE_OUT__", "to":"seqchksum_file" }, diff --git a/data/vtlib/final_output_prep.json b/data/vtlib/final_output_prep.json index 639c8107c..d718c5260 100644 --- a/data/vtlib/final_output_prep.json +++ b/data/vtlib/final_output_prep.json @@ -30,12 +30,6 @@ "postproc":{"op":"concat", "pad":"="} } }, - { - "id":"scramble_reference_flag", - "required":"no", - "comment":"flag will disappear unless scramble_reference_fasta value is given (allows unaligned cram)", - "subst_constructor":{ "vals":[ "-r", {"subst":"scramble_reference_fasta"} ] } - }, { "id":"stats_reference_flag", "required":"no", @@ -272,7 +266,7 @@ {"subst":"teepot_vflag", "ifnull":"-v"}, {"subst":"teepot_tempdir_flag"}, "-w", {"subst":"fomw_teepot_wval", "ifnull":"300"}, - {"port":"scramble", "direction":"out"}, + {"port":"bam2cram", "direction":"out"}, {"port":"flagstat", "direction":"out"}, {"port":"calibration_pu", "direction":"out"}, {"port":"bam", "direction":"out"}, @@ -305,28 +299,22 @@ "name":"c2a.json" }, { - "id":"scramble", + "id":"bam2cram", + "description":"converts BAM input (autodetected) to CRAM output", "type":"EXEC", "use_STDIN": true, "use_STDOUT": true, - "cmd":[ - "scramble", - {"subst":"b2c_mt", "ifnull":{"subst_constructor":{ "vals":[ "-t", {"subst":"b2c_mt_val"} ]}}}, - {"subst":"b2c_fmtver", "ifnull":{"subst_constructor":{ "vals":[ "-V", {"subst":"b2c_format_version"} ]}}}, - {"subst":"b2c_compress_level", "ifnull":"-7"}, - "-I", "bam", - "-O", "cram", - {"subst":"scramble_reference_flag"}, - {"select":"scramble_embed_reference","default":0,"select_range":[0,1], - "cases":[ - [], - "-e" - ] - } - ] + "cmd": [ + {"subst":"samtools_executable"}, "view", "-C", + {"subst_constructor":{"vals":[ "--threads", {"subst":"b2c_threads","ifnull":{"subst":"b2c_mt_val"}}]}}, + {"subst_constructor":{"vals":[ "--output-fmt-option", {"subst_constructor":{"vals":[ "level", {"subst":"b2c_compression_level","ifnull":7} ], "postproc":{"op":"concat", "pad":"="}}}]}}, + {"subst_constructor":{"vals":[ "-T", {"subst":"scramble_reference_fasta"}]}}, + {"subst_constructor":{"vals":[ "--output-fmt-option", {"subst_constructor":{"vals":[ "embed_ref", {"subst":"scramble_embed_reference","ifnull":0} ], "postproc":{"op":"concat", "pad":"="}}}]}}, + "-" + ] }, { - "id":"scramble_tee", + "id":"cram_tee", "type":"EXEC", "use_STDIN": true, "use_STDOUT": false, @@ -354,7 +342,7 @@ "cmd":"md5sum" }, { - "id":"scramble_md5", + "id":"create_cram_md5", "type":"EXEC", "use_STDIN": true, "use_STDOUT": true, @@ -523,16 +511,16 @@ ], "edges":[ { "id":"markdup_to_multiway", "from":"markdup", "to":"bmd_multiway" }, - { "id":"bmdmw_to_scramble", "from":"bmd_multiway:scramble", "to":"scramble" }, - { "id":"scramble_to_scramble_tee", "from":"scramble", "to":"scramble_tee" }, + { "id":"bmdmw_to_b2C", "from":"bmd_multiway:bam2cram", "to":"bam2cram" }, + { "id":"b2c_to_cram_tee", "from":"bam2cram", "to":"cram_tee" }, {"select":"c2a_switch", "required":false, "cases":{ - "on": { "id":"cramtee_to_c2a", "from":"scramble_tee:c2a", "to":"c2a" } + "on": { "id":"cramtee_to_c2a", "from":"cram_tee:c2a", "to":"c2a" } } }, - { "id":"scramble_tee_to_md5", "from":"scramble_tee:md5", "to":"scramble_md5" }, - { "id":"scramble_tee_to_crai", "from":"scramble_tee:crai", "to":"cram_index" }, - { "id":"scramble_tee_to_bscs", "from":"scramble_tee:seqchksum", "to":"cram_seqchksum" }, - { "id":"md5_to_postprocess", "from":"scramble_md5", "to":"postprocess_md5" }, + { "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":"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" }, { "id":"bmdmw_to_sts_F0xB00", "from":"bmd_multiway:samtools_stats_F0xB00", "to":"samtools_stats_F0xB00" }, { "id":"bmdmw_to_sts_F0x900_bait", "from":"bmd_multiway:samtools_stats_F0x900_bait", "to":"samtools_stats_F0x900_bait" }, @@ -552,7 +540,7 @@ { "id":"bmw_to_md5", "from":"bmd_multiway:md5", "to":"create_bam_md5" }, { "id":"md5_to_bam_postprocess", "from":"create_bam_md5", "to":"postprocess_bam_md5" }, { "id":"corrected_bam_md5_out", "from":"postprocess_bam_md5", "to":"bam_md5" }, - { "id":"tee_to_cram", "from":"scramble_tee:cram", "to":"cram_file" }, + { "id":"tee_to_cram", "from":"cram_tee:cram", "to":"cram_file" }, { "id":"corrected_md5_out", "from":"postprocess_md5", "to":"cram_md5" }, { "id":"scs_to_tee", "from":"seqchksum", "to":"seqchksum_file" }, { "id":"scs_file_to_cmp", "from":"seqchksum_file", "to":"cmp_seqchksum:bam_seqchksum" }, diff --git a/data/vtlib/final_output_prep_chrsplit_noaln.json b/data/vtlib/final_output_prep_chrsplit_noaln.json index 4821ac41e..bb5a6141a 100644 --- a/data/vtlib/final_output_prep_chrsplit_noaln.json +++ b/data/vtlib/final_output_prep_chrsplit_noaln.json @@ -30,12 +30,6 @@ "postproc":{"op":"concat", "pad":"="} } }, - { - "id":"scramble_reference_flag", - "required":"no", - "comment":"flag will disappear unless scramble_reference_fasta value is given (allows unaligned cram)", - "subst_constructor":{ "vals":[ "-r", {"subst":"scramble_reference_fasta"} ] } - }, { "id":"stats_reference_flag", "required":"no", @@ -259,7 +253,7 @@ {"subst":"teepot_vflag", "ifnull":"-v"}, {"subst":"teepot_tempdir_flag"}, "-w", {"subst":"fomw_teepot_wval", "ifnull":"300"}, - {"port":"scramble", "direction":"out"}, + {"port":"cram", "direction":"out"}, {"port":"flagstat", "direction":"out"}, {"port":"calibration_pu", "direction":"out"}, {"port":"bam", "direction":"out"}, @@ -273,28 +267,21 @@ ] }, { - "id":"scramble", + "id":"bam2cram", "type":"EXEC", "use_STDIN": true, "use_STDOUT": true, "cmd":[ - "scramble", - {"subst":"b2c_mt", "ifnull":{"subst_constructor":{ "vals":[ "-t", {"subst":"b2c_mt_val"} ]}}}, - {"subst":"b2c_fmtver", "ifnull":{"subst_constructor":{ "vals":[ "-V", {"subst":"b2c_format_version"} ]}}}, - {"subst":"b2c_compress_level", "ifnull":"-7"}, - "-I", "bam", - "-O", "cram", - {"subst":"scramble_reference_flag"}, - {"select":"scramble_embed_reference","default":0,"select_range":[0,1], - "cases":[ - [], - "-e" - ] - } + {"subst":"samtools_executable"}, "view", "-C", + {"subst_constructor":{"vals":[ "--threads", {"subst":"b2c_threads","ifnull":{"subst":"b2c_mt_val"}}]}}, + {"subst_constructor":{"vals":[ "--output-fmt-option", {"subst_constructor":{"vals":[ "level", {"subst":"b2c_compression_level","ifnull":7} ], "postproc":{"op":"concat", "pad":"="}}}]}}, + {"subst_constructor":{"vals":[ "-T", {"subst":"scramble_reference_fasta"}]}}, + {"subst_constructor":{"vals":[ "--output-fmt-option", {"subst_constructor":{"vals":[ "embed_ref", {"subst":"scramble_embed_reference","ifnull":0} ], "postproc":{"op":"concat", "pad":"="}}}]}}, + "-" ] }, { - "id":"scramble_tee", + "id":"cram_tee", "type":"EXEC", "use_STDIN": true, "use_STDOUT": false, @@ -311,7 +298,7 @@ "comment":"allow a generous 500 minutes for the teepot timeout; specify parameter value teepot_tempdir_value to specify teepot tempdir" }, { - "id":"scramble_md5", + "id":"create_cram_md5", "type":"EXEC", "use_STDIN": true, "use_STDOUT": true, @@ -452,12 +439,12 @@ "edges":[ { "id":"bamsort_to_bammarkduplicates", "from":"bamreset", "to":"bamcollate" }, { "id":"bammarkduplicates_to_multiway", "from":"bamcollate", "to":"bmd_multiway" }, - { "id":"bmdmw_to_scramble", "from":"bmd_multiway:scramble", "to":"scramble" }, - { "id":"scramble_to_scramble_tee", "from":"scramble", "to":"scramble_tee" }, - { "id":"scramble_tee_to_md5", "from":"scramble_tee:md5", "to":"scramble_md5" }, - { "id":"scramble_tee_to_crai", "from":"scramble_tee:crai", "to":"cram_index" }, - { "id":"scramble_tee_to_bscs", "from":"scramble_tee:seqchksum", "to":"cram_seqchksum" }, - { "id":"md5_to_postprocess", "from":"scramble_md5", "to":"postprocess_md5" }, + { "id":"bmdmw_to_b2c", "from":"bmd_multiway:cram", "to":"bam2cram" }, + { "id":"b2c_to_cram_tee", "from":"bam2cram", "to":"cram_tee" }, + { "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":"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" }, { "id":"bmdmw_to_sts_F0xB00", "from":"bmd_multiway:samtools_stats_F0xB00", "to":"samtools_stats_F0xB00" }, { "id":"bmdmw_to_sts_F0x900_bait", "from":"bmd_multiway:samtools_stats_F0x900_bait", "to":"samtools_stats_F0x900_bait" }, @@ -470,7 +457,7 @@ { "id":"flagstat_filter_to_flagstat", "from":"flagstat_filter", "to":"flagstat" }, { "id":"bmd_to_bam", "from":"bmd_multiway:bam", "to":"bamrecompress" }, { "id":"brc_to_bam", "from":"bamrecompress", "to":"bam_file" }, - { "id":"tee_to_cram", "from":"scramble_tee:cram", "to":"cram_file" }, + { "id":"tee_to_cram", "from":"cram_tee:cram", "to":"cram_file" }, { "id":"corrected_md5_out", "from":"postprocess_md5", "to":"cram_md5" }, { "id":"scs_to_tee", "from":"seqchksum", "to":"seqchksum_tee" }, { "id":"scs_tee_to_file", "from":"seqchksum_tee:file", "to":"seqchksum_file" }, diff --git a/data/vtlib/hisat2_alignment.json b/data/vtlib/hisat2_alignment.json index 888670d79..9f2e2a538 100644 --- a/data/vtlib/hisat2_alignment.json +++ b/data/vtlib/hisat2_alignment.json @@ -151,11 +151,10 @@ "use_STDIN":true, "use_STDOUT":true, "cmd":[ - "scramble", - {"subst":"s2b_mt", "ifnull":{"subst_constructor":{ "vals":[ "-t", {"subst":"s2b_mt_val"} ]}}}, - {"subst":"s2b_compress_level", "ifnull":"-0"}, - "-I", "sam", - "-O", "bam" + {"subst":"samtools_executable"}, "view", "-b", + {"subst_constructor":{"vals":[ "--threads", {"subst":"b2c_threads","ifnull":{"subst":"b2c_mt_val"}}]}}, + {"subst_constructor":{"vals":[ "--output-fmt-option", {"subst_constructor":{"vals":[ "level", {"subst":"s2b_compression_level","ifnull":0} ], "postproc":{"op":"concat", "pad":"="}}}]}}, + "-" ] }, { @@ -185,7 +184,7 @@ "default":2, "select_range":[1], "cases":{ "1":{}, "2":{"id":"fq2_to_quantify", "from":"fq2", "to":"quantify:fastq2"} } }, - {"id":"hisat2_to_scramble", "from":"hisat2", "to":"samtobam"}, + {"id":"hisat2_to_s2b", "from":"hisat2", "to":"samtobam"}, {"id":"samtobam_to_qname_sort", "from":"samtobam", "to":"bamsort_qname"} ] } diff --git a/data/vtlib/merge_final_output_prep.json b/data/vtlib/merge_final_output_prep.json index 6e102a619..bc6f9cfba 100644 --- a/data/vtlib/merge_final_output_prep.json +++ b/data/vtlib/merge_final_output_prep.json @@ -20,13 +20,6 @@ "comment":"this will expand to a set of subst_param elements" }, {"id":"genome_reference_fasta","required":"no"}, - { - "id":"scramble_reference_flag", - "required":"no", - "comment":"flag will disappear unless genome_reference_fasta value is given (allows unaligned cram)", - "subst_constructor":{ "vals":[ "-r", {"subst":"genome_reference_fasta"} ] - } - }, { "id":"samtools_reference_flag", "required":"no", @@ -147,7 +140,7 @@ {"subst":"teepot_vflag", "ifnull":"-v"}, {"subst":"teepot_tempdir_flag"}, "-w", {"subst":"fomw_teepot_wval", "ifnull":"7200"}, - {"port":"scramble", "direction":"out"}, + {"port":"b2c", "direction":"out"}, {"port":"flagstat", "direction":"out"}, {"port":"samtools_stats_F0x900", "direction":"out"}, {"port":"samtools_stats_F0xB00", "direction":"out"}, @@ -156,22 +149,20 @@ ] }, { - "id":"scramble", + "id":"bam2cram", "type":"EXEC", "use_STDIN": true, "use_STDOUT": true, "cmd":[ - "scramble", - {"subst":"b2c_mt", "ifnull":{"subst_constructor":{ "vals":[ "-t", {"subst":"b2c_mt_val"} ]}}}, - {"subst":"b2c_fmtver", "ifnull":{"subst_constructor":{ "vals":[ "-V", {"subst":"b2c_format_version"} ]}}}, - {"subst":"b2c_compress_level", "ifnull":"-7"}, - "-I", "bam", - "-O", "cram", - {"subst":"scramble_reference_flag"} + {"subst":"samtools_executable"}, "view", "-C", + {"subst_constructor":{"vals":[ "--threads", {"subst":"b2c_threads","ifnull":{"subst":"b2c_mt_val"}}]}}, + {"subst_constructor":{"vals":[ "--output-fmt-option", {"subst_constructor":{"vals":[ "level", {"subst":"b2c_compression_level","ifnull":7} ], "postproc":{"op":"concat", "pad":"="}}}]}}, + {"subst_constructor":{"vals":[ "-T", {"subst":"scramble_reference_fasta"}]}}, + "-" ] }, { - "id":"scramble_tee", + "id":"cram_tee", "type":"EXEC", "use_STDIN": true, "use_STDOUT": false, @@ -188,7 +179,7 @@ "comment":"allow a generous 500 minutes for the teepot timeout; specify parameter value teepot_tempdir_value to specify teepot tempdir" }, { - "id":"scramble_md5", + "id":"create_cram_md5", "type":"EXEC", "use_STDIN": true, "use_STDOUT": true, @@ -315,19 +306,19 @@ } ], "edges":[ - { "id":"bmdmw_to_scramble", "from":"bmd_multiway:scramble", "to":"scramble" }, - { "id":"scramble_to_scramble_tee", "from":"scramble", "to":"scramble_tee" }, - { "id":"scramble_tee_to_md5", "from":"scramble_tee:md5", "to":"scramble_md5" }, - { "id":"scramble_tee_to_crai", "from":"scramble_tee:crai", "to":"cram_index" }, - { "id":"scramble_tee_to_bscs", "from":"scramble_tee:seqchksum", "to":"cram_seqchksum" }, - { "id":"md5_to_postprocess", "from":"scramble_md5", "to":"postprocess_md5" }, + { "id":"bmdmw_to_b2c", "from":"bmd_multiway:b2c", "to":"bam2cram" }, + { "id":"b2c_to_cram_tee", "from":"bam2cram", "to":"cram_tee" }, + { "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":"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" }, { "id":"bmdmw_to_sts_F0xB00", "from":"bmd_multiway:samtools_stats_F0xB00", "to":"samtools_stats_F0xB00" }, { "id":"bmdmw_to_seqchksum", "from":"bmd_multiway:seqchksum", "to":"seqchksum" }, { "id":"bmdmw_to_seqchksum_extrahash", "from":"bmd_multiway:seqchksum_extrahash", "to":"seqchksum_extrahash" }, { "id":"bmdmw_to_flagstat", "from":"bmd_multiway:flagstat", "to":"flagstat_filter" }, { "id":"flagstat_filter_to_flagstat", "from":"flagstat_filter", "to":"flagstat" }, - { "id":"tee_to_cram_tears", "from":"scramble_tee:cram", "to":"cram_output" }, + { "id":"tee_to_cram_tears", "from":"cram_tee:cram", "to":"cram_output" }, { "id":"corrected_md5_out", "from":"postprocess_md5", "to":"cram_md5" }, { "id":"scs_to_tee", "from":"seqchksum", "to":"seqchksum_tee" }, { "id":"scs_tee_to_file", "from":"seqchksum_tee:file", "to":"seqchksum_file" }, diff --git a/data/vtlib/minimap2_alignment.json b/data/vtlib/minimap2_alignment.json index 53bda656e..590344370 100644 --- a/data/vtlib/minimap2_alignment.json +++ b/data/vtlib/minimap2_alignment.json @@ -76,6 +76,6 @@ ], "edges":[ { "id":"bamtofastq_to_int_fq", "from":"bamtofastq", "to":"minimap2:fq" }, - { "id":"mm2_to_scramble", "from":"minimap2", "to":"samtobam" } + { "id":"mm2_to_s2b", "from":"minimap2", "to":"samtobam" } ] } diff --git a/data/vtlib/realignment_wtsi_humansplit_notargetalign_template.json b/data/vtlib/realignment_wtsi_humansplit_notargetalign_template.json index d7c9ee3f1..8659c1fc0 100644 --- a/data/vtlib/realignment_wtsi_humansplit_notargetalign_template.json +++ b/data/vtlib/realignment_wtsi_humansplit_notargetalign_template.json @@ -295,7 +295,6 @@ { "id":"final_output_prep_target", "type":"VTFILE", - "old_comment":"inputs: _stdin_ (bam), reference_genome_fasta (for scramble); outputs: _stdout_ (bam)", "comment":"inputs: _stdin_ (bam); outputs: _stdout_ (bam)", "node_prefix":"foptgt_", "subst_map":{"phix_or_target":{"subst":"target_indicator"},"fopid":{"subst":"fopid_tgt"},"bstmp":"bsfopt","brtmp":"brfopt","bmdtmp":"bmdfopt"}, @@ -305,7 +304,6 @@ { "id":"final_output_prep_hs", "type":"VTFILE", - "old_comment":"inputs: _stdin_ (bam), reference_genome_fasta (for scramble); outputs: _stdout_ (bam)", "comment":"inputs: _stdin_ (bam); outputs: _stdout_ (bam)", "node_prefix":"fophs_", "subst_map":{"phix_or_target":{"subst":"hs_indicator"},"fopid":{"subst":"fopid_hs"},"bstmp":"bsfoph","brtmp":"brfoph","bmdtmp":"bmdfoph","scramble_reference_fasta":{"subst":"hs_reference_genome_fasta"}}, diff --git a/data/vtlib/realignment_wtsi_humansplit_template.json b/data/vtlib/realignment_wtsi_humansplit_template.json index ac6c3b3d1..23b1122c3 100755 --- a/data/vtlib/realignment_wtsi_humansplit_template.json +++ b/data/vtlib/realignment_wtsi_humansplit_template.json @@ -377,7 +377,6 @@ { "id":"final_output_prep_target", "type":"VTFILE", - "old_comment":"inputs: _stdin_ (bam), reference_genome_fasta (for scramble); outputs: _stdout_ (bam)", "comment":"inputs: _stdin_ (bam); outputs: _stdout_ (bam)", "node_prefix":"foptgt_", "subst_map":{"phix_or_target":{"subst":"target_indicator"},"fopid":{"subst":"fopid_tgt"},"bstmp":"bsfopt","brtmp":"brfopt","bmdtmp":"bmdfopt","scramble_reference_fasta":{"subst":"reference_genome_fasta"}}, @@ -387,7 +386,6 @@ { "id":"final_output_prep_hs", "type":"VTFILE", - "old_comment":"inputs: _stdin_ (bam), reference_genome_fasta (for scramble); outputs: _stdout_ (bam)", "comment":"inputs: _stdin_ (bam); outputs: _stdout_ (bam)", "node_prefix":"fophs_", "subst_map":{"phix_or_target":{"subst":"hs_indicator"},"fopid":{"subst":"fopid_hs"},"bstmp":"bsfoph","brtmp":"brfoph","bmdtmp":"bmdfoph","scramble_reference_fasta":{"subst":"hs_reference_genome_fasta"}},