Merge pull request #316 from wtsi-npg/devel

prep release 0.35.0
wtsi-npg · Apr 3, 2023 · c6a6f5c · c6a6f5c
2 parents 90ad2c8 + d45d5ed
commit c6a6f5c
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Showing 15 changed files with 99 additions and 147 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -144,32 +144,30 @@
 		"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,
 		"cmd":[ "teepot", {"subst":"teepot_vflag", "ifnull":"-v"}, {"subst":"teepot_tempdir_flag"}, "-w", "30000", "__CRAM_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",
+		"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
@@ -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" },