diff --git a/automate_demultiplex_config.py b/automate_demultiplex_config.py index 2fb3ec67..e579fb4b 100644 --- a/automate_demultiplex_config.py +++ b/automate_demultiplex_config.py @@ -8,7 +8,7 @@ import os # Set debug mode -testing = False +testing = True # =====location of input/output files===== # root of folder that contains the apps, automate_demultiplexing_logfiles and @@ -277,31 +277,31 @@ ED_cnvcalling_path = "Apps/ED_cnv_calling_v1.2.0" ED_cnvcalling_instance_type = "mem1_ssd1_v2_x4" #VCP1 exome depth -ED_readcount_normals_VCP1_file="Pan5134_normals_v1.0.0.RData" -ED_VCP1_readcount_BEDfile_pannum = "Pan5134" # just put pan number - full bedfile name is made in nexus_bedfiles function +ED_readcount_normals_VCP1_file= "project-ByfFPz00jy1fk6PjpZ95F27J:file-GZ47PPj0xygQ8z3z8yQK1qJF"#"Pan5134_normals_v1.0.0.RData" +ED_VCP1_readcount_BEDfile_pannum = "Pan5134_exomedepth.bed" #VCP2 normals data file -ED_readcount_normals_VCP2_file="Pan5132_normals_v1.0.0.RData" -ED_VCP2_readcount_BEDfile_pannum = "Pan5132" # just put pan number - full bedfile name is made in nexus_bedfiles function +ED_readcount_normals_VCP2_file="project-ByfFPz00jy1fk6PjpZ95F27J:file-GZ8ybG00bx11vq9fXP1j7QQK"#"Pan5132_normals_v1.0.0.RData" +ED_VCP2_readcount_BEDfile_pannum = "Pan5132_exomedepth.bed" #VCP3 normals data file -ED_readcount_normals_VCP3_file="Pan5149_normals_v1.0.0.RData" -ED_VCP3_readcount_BEDfile_pannum = "Pan5149" # just put pan number - full bedfile name is made in nexus_bedfiles function +ED_readcount_normals_VCP3_file=None#"Pan5149_normals_v1.0.0.RData" +ED_VCP3_readcount_BEDfile_pannum = "Pan5149_exomedepth.bed" exomedepth_refgenome_file = "project-ByfFPz00jy1fk6PjpZ95F27J:file-B6ZY7VG2J35Vfvpkj8y0KZ01" #hs37d5.fa.gz from 001 ## readcount app inputs -exomedepth_readcount_reference_genome_input="-ireference_genome=%s" % (exomedepth_refgenome_file) -exomedepth_readcount_bedfile_input="-ibedfile=" -exomedepth_readcount_normalsRdata_input="-inormals_RData=" -exomedepth_readcount_projectname_input="-iproject_name=" -exomedepth_readcount_pannumbers_input="-ibamfile_pannumbers=" -exomedepth_readcount_rdata_output="rdataout" +exomedepth_readcount_reference_genome_input=" -ireference_genome=%s" % (exomedepth_refgenome_file) +exomedepth_readcount_bedfile_input=" -ibedfile=" +exomedepth_readcount_normalsRdata_input=" -inormals_RData=" +exomedepth_readcount_projectname_input=" -iproject_name=" +exomedepth_readcount_pannumbers_input=" -ibamfile_pannumbers=" +exomedepth_readcount_rdata_output="RData" ## ED CNV calling inputs -exomedepth_cnvcalling_reference_genome_input="-ireference_genome=%s" % (exomedepth_refgenome_file) -exomedepth_cnvcalling_readcount_file_input="-ireadcount_file=" -exomedepth_cnvcalling_subpanel_bed_input="-isubpanel_bed=" -exomedepth_cnvcalling_projectname_input="-iproject_name=" -exomedepth_cnvcalling_pannumbers_input="-ibamfile_pannumbers=" +exomedepth_cnvcalling_reference_genome_input=" -ireference_genome=%s" % (exomedepth_refgenome_file) +exomedepth_cnvcalling_readcount_file_input=" -ireadcount_file=" +exomedepth_cnvcalling_subpanel_bed_input=" -isubpanel_bed=" +exomedepth_cnvcalling_projectname_input=" -iproject_name=" +exomedepth_cnvcalling_pannumbers_input=" -ibamfile_pannumbers=" # MokaWES workflow_inputs @@ -460,10 +460,10 @@ "Pan5085", # TSO500 High throughput Synnovis. no UTRS TERT promoter "Pan5112", # TSO500 High throughput BSPS. no UTRS TERT promoter "Pan5114", # TSO500 High throughput Control. no UTRS TERT promoter - "Pan4042", # STG VCP2 BRCA - TO BE REMOVED IN FUTURE UPDATE - "Pan4043", # STG VCP3 - TO BE REMOVED IN FUTURE UPDATE - "Pan4044", # STG VCP1 - TO BE REMOVED IN FUTURE UPDATE - "Pan4049", # STG VCP2 CrCa - TO BE REMOVED IN FUTURE UPDATE + #"Pan4042", # STG VCP2 BRCA - TO BE REMOVED IN FUTURE UPDATE + #"Pan4043", # STG VCP3 - TO BE REMOVED IN FUTURE UPDATE + #"Pan4044", # STG VCP1 - TO BE REMOVED IN FUTURE UPDATE + #"Pan4049", # STG VCP2 CrCa - TO BE REMOVED IN FUTURE UPDATE "Pan4119", # VCP1 Viapath R134 (FH) "Pan4121", # VCP1 Viapath R184 (CF) "Pan4122", # VCP1 Viapath R25 (FGFR) @@ -549,7 +549,7 @@ "Pan4122", "Pan4125", "Pan4126", - "Pan4044", + #"Pan4044", "Pan4821", "Pan4822", "Pan4823", @@ -572,8 +572,8 @@ "Pan4150", "Pan4129", "Pan4130", - "Pan4042", - "Pan4049", + #"Pan4042", + #"Pan4049", "Pan4816", "Pan4817", "Pan4819", @@ -599,7 +599,7 @@ "Pan4145", "Pan4146", "Pan4151", - "Pan4043", + #"Pan4043", "Pan4314", "Pan4351", "Pan4387", @@ -847,7 +847,7 @@ "RPKM_also_analyse": vcp1_panel_list, "hsmetrics_bedfile": "Pan4397data.bed", "sambamba_bedfile": "Pan4397dataSambamba.bed", - "variant_calling_bedfile": "Pan4398data.bed", + "variant_calling_bedfile": "Pan4398data.bed", # CNV not required }, "Pan4125": { # VCP1 R73 DMD (Viapath) "mokapipe": True, @@ -858,7 +858,7 @@ "hsmetrics_bedfile": "Pan4397data.bed", "sambamba_bedfile": "Pan4397dataSambamba.bed", "variant_calling_bedfile": "Pan4398data.bed", - "exome_depth_cnvcalling_BED": "Pan5135" + "exome_depth_cnvcalling_BED": "Pan4622" }, "Pan4126": { # VCP1 R337_CADASIL Viapath "mokapipe": True, @@ -868,8 +868,7 @@ "RPKM_also_analyse": vcp1_panel_list, "hsmetrics_bedfile": "Pan4397data.bed", "sambamba_bedfile": "Pan4397dataSambamba.bed", - "variant_calling_bedfile": "Pan4398data.bed", - "exome_depth_cnvcalling_BED": "Pan4549" + "variant_calling_bedfile": "Pan4398data.bed",# cnv not required }, "Pan4974": { # VCP1 Viapath (Molecular Haemostasis) R112 "mokapipe": True, @@ -1036,7 +1035,7 @@ "sambamba_bedfile": "Pan5123dataSambamba.bed", "variant_calling_bedfile": "Pan5119data.bed", "polyedge": "MSH2", - "exome_depth_cnvcalling_BED": "Pan5159" + "exome_depth_cnvcalling_BED": "Pan5160" # use R211 CNV bedfile }, "Pan4130": { # VCP2 R211 polyposis (Viapath) "mokapipe": True, @@ -1103,7 +1102,7 @@ "RPKM_also_analyse": vcp3_panel_list, "hsmetrics_bedfile": "Pan4995data.bed", "sambamba_bedfile": "Pan4995dataSambamba.bed", - "variant_calling_bedfile": "Pan4995data.bed", + "variant_calling_bedfile": "Pan4995data.bed", # CNV not required }, "Pan4134": { # VCP3 R57 (Viapath) "mokapipe": True, @@ -1113,7 +1112,7 @@ "RPKM_also_analyse": vcp3_panel_list, "hsmetrics_bedfile": "Pan4995data.bed", "sambamba_bedfile": "Pan4995dataSambamba.bed", - "variant_calling_bedfile": "Pan4995data.bed", + "variant_calling_bedfile": "Pan4995data.bed", # CNV not required }, "Pan4136": { # VCP3 R58 (Viapath) "mokapipe": True, @@ -1123,7 +1122,7 @@ "RPKM_also_analyse": vcp3_panel_list, "hsmetrics_bedfile": "Pan4995data.bed", "sambamba_bedfile": "Pan4995dataSambamba.bed", - "variant_calling_bedfile": "Pan4995data.bed", + "variant_calling_bedfile": "Pan4995data.bed",# CNV not required }, "Pan4137": { # VCP3 R60 (Viapath) "mokapipe": True, @@ -1133,7 +1132,7 @@ "RPKM_also_analyse": vcp3_panel_list, "hsmetrics_bedfile": "Pan4995data.bed", "sambamba_bedfile": "Pan4995dataSambamba.bed", - "variant_calling_bedfile": "Pan4995data.bed", + "variant_calling_bedfile": "Pan4995data.bed",# CNV not required }, "Pan4138": { # VCP3 R62 (Viapath) "mokapipe": True, @@ -1143,7 +1142,7 @@ "RPKM_also_analyse": vcp3_panel_list, "hsmetrics_bedfile": "Pan4995data.bed", "sambamba_bedfile": "Pan4995dataSambamba.bed", - "variant_calling_bedfile": "Pan4995data.bed", + "variant_calling_bedfile": "Pan4995data.bed",# CNV not required }, "Pan4143": { # VCP3 R66 (Viapath) "mokapipe": True, @@ -1154,7 +1153,7 @@ "hsmetrics_bedfile": "Pan4995data.bed", "sambamba_bedfile": "Pan4995dataSambamba.bed", "variant_calling_bedfile": "Pan4995data.bed", - "exome_depth_cnvcalling_BED": "Pan5174" + # "exome_depth_cnvcalling_BED": "Pan5174" # CNV BED not yet available }, "Pan4144": { # VCP3 R78 (Viapath) "mokapipe": True, @@ -1164,7 +1163,7 @@ "RPKM_also_analyse": vcp3_panel_list, "hsmetrics_bedfile": "Pan4995data.bed", "sambamba_bedfile": "Pan4995dataSambamba.bed", - "variant_calling_bedfile": "Pan4995data.bed", + "variant_calling_bedfile": "Pan4995data.bed",# CNV not required }, "Pan4145": { # VCP3 R79 - CMD (Viapath) "mokapipe": True, @@ -1196,7 +1195,7 @@ "RPKM_also_analyse": vcp3_panel_list, "hsmetrics_bedfile": "Pan4995data.bed", "sambamba_bedfile": "Pan4995dataSambamba.bed", - "variant_calling_bedfile": "Pan4995data.bed", + "variant_calling_bedfile": "Pan4995data.bed",# CNV not required }, "Pan4351": { # VCP3 R227 (Viapath) "mokapipe": True, @@ -1240,7 +1239,7 @@ "hsmetrics_bedfile": "Pan4995data.bed", "sambamba_bedfile": "Pan4995dataSambamba.bed", "variant_calling_bedfile": "Pan4995data.bed", - "exome_depth_cnvcalling_BED": "Pan5179", + # "exome_depth_cnvcalling_BED": "Pan5179", bedfile not yet made }, "Pan4396": { # ArcherDx (Synnovis) "archerdx": True, @@ -1318,7 +1317,7 @@ "variant_calling_bedfile": "Pan4398data.bed", "sambamba_bedfile": "Pan4397dataSambamba.bed", "STG": True, - "exome_depth_cnvcalling_BED": "Pan4703" + "exome_depth_cnvcalling_BED": "Pan4703", }, "Pan4823": { # VCP1 STG R25_FGFR "mokapipe": True, @@ -1331,7 +1330,7 @@ "hsmetrics_bedfile": "Pan4397data.bed", "variant_calling_bedfile": "Pan4398data.bed", "sambamba_bedfile": "Pan4397dataSambamba.bed", - "STG": True, + "STG": True, # CNV not required }, "Pan4824": { # VCP1 STG R73_DMD "mokapipe": True, @@ -1345,7 +1344,7 @@ "variant_calling_bedfile": "Pan4398data.bed", "sambamba_bedfile": "Pan4397dataSambamba.bed", "STG": True, - "exome_depth_cnvcalling_BED": "Pan5135" + "exome_depth_cnvcalling_BED": "Pan4622" }, "Pan4825": { # VCP1 STG R337_cadasil "mokapipe": True, @@ -1358,8 +1357,7 @@ "hsmetrics_bedfile": "Pan4397data.bed", "variant_calling_bedfile": "Pan4398data.bed", "sambamba_bedfile": "Pan4397dataSambamba.bed", - "STG": True, - "exome_depth_cnvcalling_BED": "Pan4549" + "STG": True,# CNV not required }, "Pan4826": { # VCP3 STG R56 "mokapipe": True, @@ -1371,7 +1369,7 @@ "congenica_project": "4201", "hsmetrics_bedfile": "Pan4995data.bed", "variant_calling_bedfile": "Pan4995data.bed", - "sambamba_bedfile": "Pan4995dataSambamba.bed", + "sambamba_bedfile": "Pan4995dataSambamba.bed",# CNV not required }, "Pan4827": { # VCP3 STG R57 "mokapipe": True, @@ -1383,7 +1381,7 @@ "congenica_project": "4201", "hsmetrics_bedfile": "Pan4995data.bed", "variant_calling_bedfile": "Pan4995data.bed", - "sambamba_bedfile": "Pan4995dataSambamba.bed", + "sambamba_bedfile": "Pan4995dataSambamba.bed",# CNV not required }, "Pan4828": { # VCP3 STG R58 "mokapipe": True, @@ -1395,7 +1393,7 @@ "congenica_project": "4201", "hsmetrics_bedfile": "Pan4995data.bed", "variant_calling_bedfile": "Pan4995data.bed", - "sambamba_bedfile": "Pan4995dataSambamba.bed", + "sambamba_bedfile": "Pan4995dataSambamba.bed",# CNV not required }, "Pan4829": { # VCP3 STG R60 "mokapipe": True, @@ -1407,7 +1405,7 @@ "congenica_project": "4201", "hsmetrics_bedfile": "Pan4995data.bed", "variant_calling_bedfile": "Pan4995data.bed", - "sambamba_bedfile": "Pan4995dataSambamba.bed", + "sambamba_bedfile": "Pan4995dataSambamba.bed",# CNV not required }, "Pan4830": { # VCP3 STG R62 "mokapipe": True, @@ -1419,7 +1417,7 @@ "congenica_project": "4201", "hsmetrics_bedfile": "Pan4995data.bed", "variant_calling_bedfile": "Pan4995data.bed", - "sambamba_bedfile": "Pan4995dataSambamba.bed", + "sambamba_bedfile": "Pan4995dataSambamba.bed",# CNV not required }, "Pan4831": { # VCP3 STG R66 "mokapipe": True, @@ -1432,7 +1430,7 @@ "hsmetrics_bedfile": "Pan4995data.bed", "variant_calling_bedfile": "Pan4995data.bed", "sambamba_bedfile": "Pan4995dataSambamba.bed", - "exome_depth_cnvcalling_BED": "Pan5174" + # "exome_depth_cnvcalling_BED": "Pan5174" BEDfile not yet available }, "Pan4832": { # VCP3 STG R78 "mokapipe": True, @@ -1444,7 +1442,7 @@ "congenica_project": "4201", "hsmetrics_bedfile": "Pan4995data.bed", "variant_calling_bedfile": "Pan4995data.bed", - "sambamba_bedfile": "Pan4995dataSambamba.bed", + "sambamba_bedfile": "Pan4995dataSambamba.bed",# CNV not required }, "Pan4833": { # VCP3 STG R79 "mokapipe": True, @@ -1457,7 +1455,7 @@ "hsmetrics_bedfile": "Pan4995data.bed", "variant_calling_bedfile": "Pan4995data.bed", "sambamba_bedfile": "Pan4995dataSambamba.bed", - "exome_depth_cnvcalling_BED": "Pan5168" + "exome_depth_cnvcalling_BED": "Pan5168", }, "Pan4834": { # VCP3 STG R81 "mokapipe": True, @@ -1482,7 +1480,7 @@ "congenica_project": "4201", "hsmetrics_bedfile": "Pan4995data.bed", "variant_calling_bedfile": "Pan4995data.bed", - "sambamba_bedfile": "Pan4995dataSambamba.bed", + "sambamba_bedfile": "Pan4995dataSambamba.bed",# CNV not required }, "Pan4836": { # VCP3 STG R229 "mokapipe": True, @@ -1495,7 +1493,7 @@ "hsmetrics_bedfile": "Pan4995data.bed", "variant_calling_bedfile": "Pan4995data.bed", "sambamba_bedfile": "Pan4995dataSambamba.bed", - "exome_depth_cnvcalling_BED": "Pan5179" + #"exome_depth_cnvcalling_BED": "Pan5179" BEDfile not yet available }, "Pan4819": { # VCP2 STG R210 "mokapipe": True, @@ -1509,7 +1507,7 @@ "variant_calling_bedfile": "Pan5119data.bed", "sambamba_bedfile": "Pan5123dataSambamba.bed", "polyedge": "MSH2", - "exome_depth_cnvcalling_BED": "Pan5159" + "exome_depth_cnvcalling_BED": "Pan5160" # useR211 bedfile }, "Pan4820": { # VCP2 STG R211 "mokapipe": True, diff --git a/demultiplex.py b/demultiplex.py index 78575b11..35d7e160 100644 --- a/demultiplex.py +++ b/demultiplex.py @@ -213,7 +213,7 @@ def already_demultiplexed(self, runfolder): self.samplesheet = self.runfolder + "_SampleSheet.csv" self.samplesheet_path = os.path.join(config.samplesheets_dir, self.samplesheet) # if development run skip the samplesheet check to avoid endless alerts - if not self.check_for_development_run(): + if not self.check_for_development_run(self.samplesheet_path): # run samplesheet checks (uses try to ensure that should an error occur this doesn't affect the other # script functionality ss_verification_results = samplesheet_verifier.run_ss_checks(self.samplesheet_path) @@ -242,7 +242,7 @@ def check_for_development_run(self,samplesheet_path): """ sample_list = [] - with open(self.runfolder_obj.runfolder_samplesheet_path, "r") as samplesheet_stream: + with open(samplesheet_path, "r") as samplesheet_stream: # read the file into a list and loop through the list in reverse (bottom to top). # this allows us to access the sample names, and stop when reach the column headers, skipping the header of the file. for line in reversed(samplesheet_stream.readlines()): diff --git a/upload_and_setoff_workflows.py b/upload_and_setoff_workflows.py index 8ba38a62..4ec167ef 100644 --- a/upload_and_setoff_workflows.py +++ b/upload_and_setoff_workflows.py @@ -252,6 +252,7 @@ def __init__(self, runfolder, now, debug_mode=False): # arguments to capture jobids self.depends_list = 'depends_list="${depends_list} -d ${jobid} "' + self.depends_list_ED_readcount = 'depends_list="${depends_list} -d ${EDjobid} "' self.depends_list_gatk = 'depends_list_gatk="${depends_list_gatk} -d ${jobid} "' self.depends_list_recombined = 'depends_list="${depends_list} ${depends_list_gatk} "' # Argument to define depends_list only if the job ID exists @@ -632,8 +633,8 @@ def check_for_development_run(self): sample_list = [] # build list of development pan numbers development_panel_list=[] - for pan in self.panel_dictionary: - if pan["development_run"]: + for pan in self.panel_dictionary.keys(): + if self.panel_dictionary[pan]["development_run"]: development_panel_list.append(pan) with open( @@ -1396,13 +1397,7 @@ def nexus_bedfiles(self, pannumber): + self.panel_dictionary[pannumber]["RPKM_bedfile_pan_number"] + "_RPKM.bed" ) - if self.panel_dictionary[pannumber]["exome_depth_readcount_BED"]: - bed_dict["ED_readcount_bedfile"] = ( - config.app_project - + config.bedfile_folder - + self.panel_dictionary[pannumber]["exome_depth_readcount_BED"] - + "exomedepth.bed" - ) + if self.panel_dictionary[pannumber]["exome_depth_cnvcalling_BED"]: bed_dict["exome_depth_cnvcalling_BED"] = ( config.app_project @@ -1410,6 +1405,7 @@ def nexus_bedfiles(self, pannumber): + self.panel_dictionary[pannumber]["exome_depth_cnvcalling_BED"] + "_CNV.bed" ) + return bed_dict def start_building_dx_run_cmds(self): @@ -1626,11 +1622,12 @@ def determine_exome_depth_requirements(self,pannnumber_list): List of dx run commands """ + # generate list of pan numbers in samplenames to process in ED VCP1=[] VCP2=[] VCP3=[] command_list=[] - # could prob do list comprehension here + for pannumber in set(pannnumber_list): # not all VCP1/2/3 pan numbers need CNV calling if self.panel_dictionary[pannumber]["exome_depth_cnvcalling_BED"]: @@ -1646,7 +1643,7 @@ def determine_exome_depth_requirements(self,pannnumber_list): # first build readcount command. command_list.append(self.build_ED_readcount_cmd(set(VCP1), config.ED_readcount_normals_VCP1_file,config.ED_VCP1_readcount_BEDfile_pannum)) # The output of readcount can be used in multiqc so add this to the multiqc depends list - command_list.append(self.add_to_depends_list("exomedepth", 'depends_list')) + command_list.append(self.add_to_depends_list("exomedepth", 'depends_list_ED_readcount')) # the cnvcalling stage can use the jobid from the readcount stage as an input so run these before the next capture panel for panel in set(VCP1):# then build cnvcalling commands command_list.append(self.build_ED_cnv_calling_cmd(panel)) @@ -1654,14 +1651,14 @@ def determine_exome_depth_requirements(self,pannnumber_list): if len(VCP2)>2: # first build readcount command command_list.append(self.build_ED_readcount_cmd(set(VCP2), config.ED_readcount_normals_VCP2_file,config.ED_VCP2_readcount_BEDfile_pannum)) - command_list.append(self.add_to_depends_list("exomedepth", 'depends_list')) + command_list.append(self.add_to_depends_list("exomedepth", 'depends_list_ED_readcount')) for panel in set(VCP2):# then build cnvcalling commands command_list.append(self.build_ED_cnv_calling_cmd(panel)) if len(VCP3)>2: # first build readcount command command_list.append(self.build_ED_readcount_cmd(set(VCP3), config.ED_readcount_normals_VCP3_file,config.ED_VCP3_readcount_BEDfile_pannum)) - command_list.append(self.add_to_depends_list("exomedepth", 'depends_list')) + command_list.append(self.add_to_depends_list("exomedepth", 'depends_list_ED_readcount')) for panel in set(VCP2):# then build cnvcalling commands command_list.append(self.build_ED_cnv_calling_cmd(panel)) @@ -1678,15 +1675,13 @@ def build_ED_readcount_cmd(self,pannumber_list, normals_file,readcount_bedfile_p dx run cmd (string) """ #build bedfile address from the readcount_bedfile_pannum input - bedfiles = self.nexus_bedfiles(readcount_bedfile_pannum) - readcount_bedfile=bedfiles["exome_depth_readcount_BED"] + readcount_bedfile = "%s%s%s" % (config.app_project,config.bedfile_folder,readcount_bedfile_pannum) dx_command_list = [ self.ED_readcount_command, config.exomedepth_readcount_reference_genome_input, config.exomedepth_readcount_bedfile_input, readcount_bedfile, - config.exomedepth_cnvcalling_subpanel_bed_input, config.exomedepth_readcount_normalsRdata_input, normals_file, config.exomedepth_readcount_projectname_input, @@ -1709,13 +1704,13 @@ def build_ED_cnv_calling_cmd(self,pannumber): Returns: dx run cmd (string) """ - # build bedfile address using the given pan number extract exome_depth_cnvcalling_BED from panel config dict + # pull out the appropriate bedfile for ED cnvcalling app BEDfrom panel config dict (exome_depth_cnvcalling_BED) + # note the Pan number for this BED will be different to that used to name the sample bedfiles = self.nexus_bedfiles(pannumber) ed_cnvcalling_bedfile = bedfiles["exome_depth_cnvcalling_BED"] dx_command_list = [ self.ED_cnvcalling_command, - config.exomedepth_cnvcalling_reference_genome_input, config.exomedepth_cnvcalling_readcount_file_input, "$EDjobid:%s" % (config.exomedepth_readcount_rdata_output), config.exomedepth_cnvcalling_subpanel_bed_input, @@ -2364,6 +2359,8 @@ def add_to_depends_list(self, fastq, depends_type): return self.depends_list_gatk elif depends_type=='depends_list_recombined': return self.depends_list_recombined + elif depends_type=='depends_list_ED_readcount': + return self.depends_list_ED_readcount def create_multiqc_command(self): """