diff --git a/xtea/gnrt_pipeline_germline_cloud_v38.py b/xtea/gnrt_pipeline_germline_cloud_v38.py index b27e40f..a159c7c 100644 --- a/xtea/gnrt_pipeline_germline_cloud_v38.py +++ b/xtea/gnrt_pipeline_germline_cloud_v38.py @@ -98,7 +98,7 @@ def gnrt_calling_command(s_family_id, iclip_c, iclip_rp, idisc_c, iflt_clip, ifl "-r ${{L1_CNS}} --ref ${{REF}} -a ${{ANNOTATION}} " \ "-o ${{PREFIX}}\"candidate_disc_filtered_cns.txt\" {4} {5} {6} {7}\n".format(iflt_clip, iflt_disc, iflk_len, ncores, s_purity, s_user, s_tumor, s_resume) if b_SVA==True: - s_filter = "python ${{XTEA_PATH}}\"x_TEA_main_denovo_cloud.py\" -N --sva --cr {0} --nd {1} -b ${{BAM_LIST}} -p ${{TMP_CNS}} " \ + s_filter = "python ${{XTEA_PATH}}\"x_TEA_main_germline_cloud.py\" -N --sva --cr {0} --nd {1} -b ${{BAM_LIST}} -p ${{TMP_CNS}} " \ "--fflank ${{SF_FLANK}} --flklen {2} -n {3} -i ${{PREFIX}}\"candidate_list_from_disc.txt\" " \ "-r ${{L1_CNS}} --ref ${{REF}} -a ${{ANNOTATION}} " \ "-o ${{PREFIX}}\"candidate_disc_filtered_cns.txt\" {4} {5} {6} {7}\n".format(iflt_clip, iflt_disc, iflk_len, @@ -126,7 +126,7 @@ def gnrt_calling_command(s_family_id, iclip_c, iclip_rp, idisc_c, iflt_clip, ifl " -n {0} -i ${{PREFIX}}\"candidate_disc_filtered_cns.txt.high_confident.post_filtering.txt\" " \ " --ref ${{REF}} -o ${{PREFIX}}\"assembled_ins_sequence.fa\" \n".format(ncores) if b_tumor==True: - sf_sr_asm = "python ${{XTEA_PATH}}\"x_TEA_main_denovo_cloud.py\" --sr_asm -b ${{BAM_LIST}} -p ${{TMP_CNS}}\"asm\" " \ + sf_sr_asm = "python ${{XTEA_PATH}}\"x_TEA_main_germline_cloud.py\" --sr_asm -b ${{BAM_LIST}} -p ${{TMP_CNS}}\"asm\" " \ " -n {0} -i ${{PREFIX}}\"candidate_disc_filtered_cns_high_confident_post_filtering_somatic.txt\" " \ " --ref ${{REF}} -o ${{PREFIX}}\"assembled_ins_sequence.fa\" \n".format(ncores) ####