bam-only starts with updated sample ids crash due to sample id mismatch between ped and vcf in inher_models + other mismatches

[alkc]

Discovered when tinkering with #169

Error occurs when some sample A is started with updated id (in input CSV) e.g. A-20240926 from bam file A_dedup.bam

In the example below GIAB-NA24385-D1-230622-20240926 is the sample id in the CSV, while the bam file which the sample is started from is GIAB-NA24385-D1-230622_dedup.bam

Error executing process > 'inher_models (GIAB-NA24385-D1-230622-20240926)'                                                                             
                                                                                                                                                       
Caused by:                                                                                                                                             
  Process `inher_models (GIAB-NA24385-D1-230622-20240926)` terminated with an error exit status (1)                                                    
                                                                                                                                                       
Command executed:                                                                                                                                      
                                                                                                                                                       
  genmod models GIAB-NA24385-D1-230622-20240926.cadd.vcf -p 3 -f GIAB-NA24385-D1-230622-20240926_base.ped > GIAB-NA24385-D1-230622-20240926.models.vcf 
                                                                                                                                                       
  cat <<-END_VERSIONS > inher_models_versions.yml                                                                                                      
  inher_models:                                                                                                                                        
      genmod: $(echo $(genmod --version 2>&1) | sed -e "s/^.*genmod version: //")                                                                      
  END_VERSIONS                                                                                                                                         
                                                                                                                                                       
Command exit status:                                                                                                                                   
  1                                                                                                                                                    
                                                                                                                                                       
Command output:                                                                                                                                        
  (empty)                                                                                                                                              
                                                                                                                                                       
Command error:                                                                                                                                         
  [2024-09-26 10:38:54,526] ERROR   : genmod.commands.annotate_models: Individuals in PED file must exist in VCF file                                  
  Aborted!                                                                                                                                             
                                                                                                                                                       
Work dir:                                                                                                                                              
  /mnt/beegfs/nextflow/GIAB-NA24385-D1-230622-20240926.alkc_PR_test_wgs/41/c62b23fa74977ce43108708a9596e3                                              
                                                                                                                                                       
Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`                                  

Mismatch exists in more VCFs:

┌──alkc@rs-fe1 /mnt/beegfs/nextflow/GIAB-NA24385-D1-230622-20240926.alkc_PR_test_wgs
└─$ find . -name '*.vcf' -type f | xargs -I _ sh -c  'echo -e "_\t$(grep ^#CHROM _ | cut -f 10)"' | column -t
./71/75a95db7858462be672074ef288fac/GIAB-NA24385-D1-230622-20240926.eh.vcf                                                GIAB_HG002_dedup <------- Name of the GIAB bam symlink specified in CSV
./f4/e9596b4d0da226daab1fa73546dbe8/workspace/svHyGen/candidateSV.0000.vcf
./f4/e9596b4d0da226daab1fa73546dbe8/workspace/svHyGen/diploidSV.0000.vcf                                                  GIAB-NA24385-D1-230622 <- Actual basename of the input BAM
./85/f4b553b034bdcb2472b94c52e9c60d/GIAB-NA24385-D1-230622-20240926.tiddit.vcf                                            GIAB-NA24385-D1-230622
./85/f4b553b034bdcb2472b94c52e9c60d/GIAB-NA24385-D1-230622-20240926.tiddit.filtered.vcf                                   GIAB-NA24385-D1-230622
./1f/32b89e727df3fa985bf5a57fde0d5c/GIAB-NA24385-D1-230622-20240926.mutect2.vcf                                           GIAB-NA24385-D1-230622
./53/63afcf1a1fe5beabf06f7a36d848ca/GIAB-NA24385-D1-230622-20240926.mutect2.adjusted.vcf                                  GIAB-NA24385-D1-230622
./53/63afcf1a1fe5beabf06f7a36d848ca/GIAB-NA24385-D1-230622-20240926.mutect2.breakmulti.filtered5p.vcf                     GIAB-NA24385-D1-230622
./53/63afcf1a1fe5beabf06f7a36d848ca/GIAB-NA24385-D1-230622-20240926.mutect2.breakmulti.filtered5p.0genotyped.vcf          GIAB-NA24385-D1-230622
./53/63afcf1a1fe5beabf06f7a36d848ca/GIAB-NA24385-D1-230622-20240926.mutect2.breakmulti.filtered5p.0genotyped.proband.vcf  GIAB-NA24385-D1-230622
./ad/bd46eb7c0ad06e99f288cc62a370cf/GIAB-NA24385-D1-230622.hg2.vcf
./4d/95ab2e449dc1acf48de9ec99b878df/GIAB-NA24385-D1-230622-20240926.fixinfo.vcf                                           GIAB-NA24385-D1-230622
./a3/51c2112bb0b902fed3270aa2abf2be/GIAB-NA24385-D1-230622-20240926.eh.stranger.vcf                                       GIAB_HG002_dedup
./a3/51c2112bb0b902fed3270aa2abf2be/GIAB-NA24385-D1-230622-20240926.fixinfo.eh.stranger.vcf                               GIAB_HG002_dedup
./6f/fd3c90d23529d60accabdb9ed16778/GIAB-NA24385-D1-230622-20240926.fixinfo.eh.stranger.vcf.rename.vcf                    GIAB-NA24385-D1-230622-20240926 <-- The only one that is correct :D
./cc/4cbe31c05cef634fc9e7a05822ae33/GIAB-NA24385-D1-230622-20240926.combined.vcf                                          GIAB-NA24385-D1-230622
./99/10528a9c47fba47716cc08ac79e26b/GIAB-NA24385-D1-230622-20240926.multibreak.vcf                                        GIAB-NA24385-D1-230622
./99/10528a9c47fba47716cc08ac79e26b/GIAB-NA24385-D1-230622-20240926.norm.vcf                                              GIAB-NA24385-D1-230622
./99/10528a9c47fba47716cc08ac79e26b/GIAB-NA24385-D1-230622-20240926.norm.uniq.vcf                                         GIAB-NA24385-D1-230622
./99/10528a9c47fba47716cc08ac79e26b/GIAB-NA24385-D1-230622-20240926.norm.uniq.DPAF.vcf                                    GIAB-NA24385-D1-230622
./99/10528a9c47fba47716cc08ac79e26b/GIAB-NA24385-D1-230622-20240926.intersected_diploid.vcf                               GIAB-NA24385-D1-230622
./99/10528a9c47fba47716cc08ac79e26b/GIAB-NA24385-D1-230622-20240926.intersected.vcf                                       GIAB-NA24385-D1-230622
./52/006b7a54dae9151036b5c8bd1f6e21/GIAB-NA24385-D1-230622-20240926.only_indels.vcf                                       GIAB-NA24385-D1-230622
./0d/7ee70bf9303d738d25c3e2220aa775/GIAB-NA24385-D1-230622-20240926.SNPs.vcf                                              GIAB-NA24385-D1-230622
./c7/2c377d3557d173154f664e971aa6b1/GIAB-NA24385-D1-230622-20240926.vep.vcf                                               GIAB-NA24385-D1-230622
./b0/6b5bc95a72c3155266c2610c8f4181/GIAB-NA24385-D1-230622-20240926.only_indels.vep.vcf                                   GIAB-NA24385-D1-230622
./b0/6b5bc95a72c3155266c2610c8f4181/GIAB-NA24385-D1-230622-20240926.only_indels.vep.filtered.vcf                          GIAB-NA24385-D1-230622
./41/c62b23fa74977ce43108708a9596e3/GIAB-NA24385-D1-230622-20240926.models.vcf <------------------------------------------------------------------------------ Empty due to crash
./db/0ec474c7f04aa827f2a96949d3dea2/GIAB-NA24385-D1-230622-20240926.clinvar.loqusdb.gene.vcf                              GIAB-NA24385-D1-230622
./ed/7fde6c48ef0130b7596fdbb15fe09c/GIAB-NA24385-D1-230622-20240926.mod.vcf                                               GIAB-NA24385-D1-230622
./54/c865c3759dc0c37f3568db7d5a5ff2/GIAB-NA24385-D1-230622-20240926.marksplice.vcf                                        GIAB-NA24385-D1-230622
./ef/2ab627195f7ee26316b6b627545fb4/GIAB-NA24385-D1-230622-20240926.cadd.vcf                                              GIAB-NA24385-D1-230622 <------------ Crashes genmod inher models