# Pipelines & tools
| Type | Command | Container | mtime | |
|---|---|---|---|---|
| alignMerge | pipeline | bwaAlign+mergeBamDup | NA | 2021-10-25 12:58:44 |
| AnnPhaseVcf | pipeline | VCFvep+dVCFcoverage+rVCFcoverage+VCFexpression+PhaseVcf | NA | 2022-02-16 11:36:10 |
| BaseRecal | pipeline | BaseRecalibrator+ApplyBQSR+samtools_index+samtools_flagstat+samtools_stats | NA | 2021-10-25 12:58:44 |
| bwa_align | pipeline | bwa+sam2bam+sortBam+idxBam | NA | 2022-07-27 11:04:03 |
| bwaAlign | pipeline | bwa+sam2bam+sortBam+idxBam | NA | 2022-02-16 11:36:10 |
| bwaDup | pipeline | bwaAlign+mergeBam+markdup+samtools_index+samtools_flagstat+samtools_stats+md5sum | NA | 2022-07-27 11:04:50 |
| bwaMM | pipeline | bwaAlign+mergeBamDup | NA | 2022-02-16 11:36:10 |
| bwaMMRecal | pipeline | bwaAlign+mergeBamDup+BaseRecal | NA | 2021-10-25 12:58:44 |
| bwaMRecal | pipeline | bwaAlign+markdup+BaseRecal | NA | 2021-10-25 12:58:44 |
| CombineGenotypeGVCFs | pipeline | CombineGVCFs+GenotypeGVCFs | NA | 2021-10-25 12:58:44 |
| COMPSRA_rn | pipeline | copy+compsra | NA | 2021-10-25 14:07:37 |
| delly_somatic | pipeline | dellyCall+listSample+echo+fpaste+dellyFilter | NA | 2021-10-25 12:58:44 |
| GAlign | pipeline | fqJson+fq2ubam+ubam2bamJson+align+mvOut | NA | 2021-10-25 12:58:44 |
| glnexus_joint | pipeline | glnexus+bcf | NA | 2022-06-16 17:40:40 |
| GPoN | pipeline | GenomicsDB+PoN | NA | 2021-10-25 14:07:37 |
| hapCall | pipeline | hapJson+HC+mvOut | NA | 2021-10-25 12:58:44 |
| jdCall | pipeline | jdJson+JD+mvOut | NA | 2021-10-25 12:58:44 |
| lancet_scatter | pipeline | lancet_bed+mergeVcf | NA | 2021-10-25 14:07:37 |
| lofreq_indel | pipeline | indelq+bamIdx | NA | 2021-10-25 12:58:44 |
| lofreq_realign | pipeline | realign+sortBam+indelq+bamIdx | NA | 2022-02-16 11:36:10 |
| LoFreqPL | pipeline | tbamR+nbamR+lofreqCall | NA | 2021-10-25 12:58:44 |
| LoFreqSI | pipeline | tbamR+nbamR+lofreqCall | NA | 2021-10-25 12:58:44 |
| lumpy | pipeline | discord+sam+split+sam2bam+discord_idx+split_idx+lumpy | NA | 2022-06-16 17:40:40 |
| mantaStrelka | pipeline | manta+strelka | NA | 2021-10-25 12:58:44 |
| mergeBamDup | pipeline | mergeBam+markdup+samtools_index+samtools_flagstat | NA | 2021-10-25 12:58:44 |
| miRDeep2PL | pipeline | Mapper+miRDeep2 | NA | 2021-10-25 12:58:44 |
| MuSE_scatter | pipeline | MuSEchr+mergeVcf+sortVcf+normVcf | NA | 2021-10-25 14:07:37 |
| Mutect2PL | pipeline | Mutect2+GetPileupSummariesT+GetPileupSummariesN+CalculateContamination+LearnReadOrientationModel+FilterMutectCalls+bcfview | NA | 2021-10-25 14:07:37 |
| neusomatic | pipeline | preprocess+call+postprocess | NA | 2021-10-25 12:58:44 |
| phaseVcf | pipeline | splitSample+renameGVcf+renameSVcf+combineVariants+sortVcf+ReadBackedPhasing+bgzip+tabixIndex | NA | 2021-10-25 12:58:44 |
| rnaseq_quant | pipeline | STAR+sortBam+samtools_index+samtools_flagstat+featureCounts+gtfToGenePred+genePredToBed+r_distribution+salmon | NA | 2022-02-16 11:36:10 |
| rnaseq_Sf | pipeline | fastqc+STAR+sortBam+samtools_index+samtools_flagstat+featureCounts+gtfToGenePred+genePredToBed+r_distribution+gCoverage | NA | 2021-10-25 14:07:38 |
| RSeQC | pipeline | gtfToGenePred+genePredToBed+r_distribution+gCoverage | NA | 2021-10-25 12:58:44 |
| ScarHRD | pipeline | bam2seqz+seqz_binning+hrd | NA | 2022-06-16 17:40:40 |
| SomaticCaller_mouse | pipeline | Mutect2+MuSE+bgzip+tabixIndex+mantaStrelka+VarDict+combine | NA | 2022-08-16 00:08:09 |
| SomaticCaller4 | pipeline | Mutect2PL+MuSE+bgzip+tabixIndex+mantaStrelka+VarDict+combine | NA | 2022-06-24 15:39:37 |
| SomaticCallers | pipeline | Mutect2PL+MuSE+bgzip+tabixIndex+mantaStrelka+SomaticSniper+VarDict+VarScanPL+Wrapper+mergeTSV+neusomaticPL | NA | 2021-10-25 14:07:37 |
| STARsoloDropletUtils | pipeline | STARsolo+DropletUtils | NA | 2022-07-27 11:29:33 |
| strelka2PL | pipeline | manta+strelka+strelkaSNV+strelkaIndel | NA | 2021-10-25 12:58:44 |
| SUPPA | pipeline | quantMerge+genEvents+mergeEvents+psiPerEvent+splitEventsG1+splitEventsG2+splitExpG1+splitExpG2+diffSplice | NA | 2021-10-25 12:58:44 |
| targetVarCall | pipeline | bwaAlign+BaseRecal+bedtolist+HaplotypeCaller+GenotypeGVCFs | NA | 2021-10-25 12:58:44 |
| VarScan2Somatic | pipeline | mpileupT+mpileupN+somatic+processSomatic+somaticFilter | NA | 2021-10-25 12:58:44 |
| vcf_index | pipeline | bgzip+index | NA | 2021-10-25 12:58:44 |
| vcfCoverage | pipeline | decompose+readcount+readcount_annotator_snv+readcount_annotator_indel | NA | 2021-10-25 12:58:44 |
| vcfExpression | pipeline | kallistoQuant+cleanExp+vcfExpAnn+T2Gene+vcfgExpAnn+bgzip+tabixIndex | NA | 2022-06-16 17:40:40 |
| vcfSubBam | pipeline | vcf2bed+subBam+idxBam | NA | 2021-10-25 14:07:38 |
| tl_annovar | tool | table_annovar.pl | bioinfochrustrasbourg/annovar | 2021-10-25 12:58:45 |
| tl_ApplyBQSR | tool | gatk ApplyBQSR | broadinstitute/gatk:latest | 2021-10-25 12:58:44 |
| tl_awk_merge | tool | awk | NA | 2021-10-25 12:58:45 |
| tl_bam_readcount | tool | /usr/bin/python /usr/bin/bam_readcount_helper.py | mgibio/bam_readcount_helper-cwl:1.1.1 | 2021-10-25 12:58:45 |
| tl_bam_stat.py | tool | bam_stat.py | quay.io/biocontainers/rseqc:4.0.0--py38h4a8c8d9_1 | 2021-10-25 14:07:38 |
| tl_bam2seqz | tool | sequenza-utils bam2seqz | quay.io/biocontainers/sequenza-utils:3.0.0--py39h67e14b5_5 | 2022-06-16 17:40:40 |
| tl_bamCoverage | tool | bamCoverage | quay.io/biocontainers/deeptools:3.4.3--py_0 | 2021-10-25 12:58:45 |
| tl_BaseRecalibrator | tool | gatk BaseRecalibrator | broadinstitute/gatk:latest | 2021-10-25 12:58:44 |
| tl_bcftools_concat | tool | bcftools concat | quay.io/biocontainers/bcftools:1.13--h3a49de5_0 | 2021-10-25 14:07:38 |
| tl_bcftools_norm | tool | bcftools norm | quay.io/biocontainers/bcftools:1.13--h3a49de5_0 | 2021-10-25 14:07:38 |
| tl_bcftools_query | tool | bcftools query | quay.io/biocontainers/bcftools:1.13--h3a49de5_0 | 2021-10-25 14:07:38 |
| tl_bcftools_reheader | tool | bcftools reheader | quay.io/biocontainers/bcftools:1.13--h3a49de5_0 | 2021-10-25 14:07:38 |
| tl_bcftools_sort | tool | bcftools sort | quay.io/biocontainers/bcftools:1.13--h3a49de5_0 | 2021-10-25 14:07:38 |
| tl_bcftools_view | tool | bcftools view | quay.io/biocontainers/bcftools:1.13--h3a49de5_0 | 2021-10-25 14:07:38 |
| tl_bcfview | tool | bcftools view | biocontainers/bcftools:v1.5_cv3 | 2021-10-25 12:58:45 |
| tl_BedToIntervalList | tool | picard BedToIntervalList | quay.io/biocontainers/picard:2.21.1--0 | 2021-10-25 12:58:44 |
| tl_bedtools_genomecov | tool | bedtools genomecov | quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0 | 2021-10-25 12:58:45 |
| tl_bgzip | tool | bgzip -c | biocontainers/tabix:v1.3.2-2-deb_cv1 | 2021-10-25 12:58:45 |
| tl_bigWigToWig | tool | bigWigToWig | biowardrobe2/ucscuserapps:v358_2 | 2021-10-25 12:58:45 |
| tl_bismark_methylation_extractor | tool | bismark_methylation_extractor | quay.io/biocontainers/bismark:0.23.1--hdfd78af_0 | 2022-06-16 17:40:40 |
| tl_bismark | tool | bismark | quay.io/biocontainers/bismark:0.23.1--hdfd78af_0 | 2022-06-16 17:40:40 |
| tl_blastn | tool | blastn | biocontainers/blast:v2.2.31_cv2 | 2021-10-25 12:58:45 |
| tl_bowtie_build | tool | bowtie-build | biocontainers/bowtie:v1.2.2dfsg-4-deb_cv1 | 2021-10-25 12:58:45 |
| tl_bowtie2_build | tool | bowtie2-build | biocontainers/bowtie2:v2.2.9_cv2 | 2021-10-25 12:58:45 |
| tl_bowtie2 | tool | bowtie2 | biocontainers/bowtie2:v2.2.9_cv2 | 2021-10-25 12:58:45 |
| tl_bwa_index | tool | bwa index | biocontainers/bwa:v0.7.17-3-deb_cv1 | 2021-10-25 12:58:45 |
| tl_bwa | tool | bwa mem | biocontainers/bwa:v0.7.17-3-deb_cv1 | 2021-10-25 12:58:45 |
| tl_CalculateContamination | tool | gatk CalculateContamination | broadinstitute/gatk:latest | 2021-10-25 12:58:44 |
| tl_Cat | tool | cat | NA | 2021-10-25 12:58:44 |
| tl_cnv_facets | tool | cnv_facets.R | hubentu/facets:0.6.2 | 2022-06-16 17:40:40 |
| tl_cnvkit_batch | tool | cnvkit.py batch | etal/cnvkit | 2021-10-25 12:58:45 |
| tl_CollectGcBiasMetrics | tool | picard CollectGcBiasMetrics | quay.io/biocontainers/picard:2.26.4--hdfd78af_0 | 2022-02-16 11:36:10 |
| tl_CollectInsertSizeMetrics | tool | picard CollectInsertSizeMetrics | quay.io/biocontainers/picard:2.21.1--0 | 2021-10-25 12:58:44 |
| tl_ColSeqArtifact | tool | gatk CollectSequencingArtifactMetrics | broadinstitute/gatk:latest | 2021-10-25 12:58:44 |
| tl_CombineGVCFs | tool | gatk CombineGVCFs | broadinstitute/gatk:latest | 2021-10-25 12:58:44 |
| tl_CombineVariants | tool | java -jar /usr/GenomeAnalysisTK.jar -T CombineVariants | broadinstitute/gatk3:3.8-1 | 2021-10-25 12:58:44 |
| tl_COMPSRA | tool | java -jar /opt/COMPSRA.jar | hubentu/compsra | 2021-10-25 14:07:38 |
| tl_convert2bed | tool | convert2bed | quay.io/biocontainers/bedops:2.4.39--h7d875b9_1 | 2021-10-25 12:58:45 |
| tl_cp | tool | cp | NA | 2021-10-25 14:07:38 |
| tl_CREST | tool | /opt/CREST/CREST.sh | hubentu/crest | 2021-10-25 12:58:44 |
| tl_cutadapt | tool | cutadapt | kfdrc/cutadapt | 2021-10-25 14:07:38 |
| tl_deepvariant | tool | /opt/deepvariant/bin/run_deepvariant | google/deepvariant | 2021-10-25 12:58:45 |
| tl_delly_call | tool | delly call | quay.io/biocontainers/delly:0.8.7--he03298f_1 | 2022-06-16 17:40:40 |
| tl_delly_filter | tool | delly filter | quay.io/biocontainers/delly:0.8.7--he03298f_1 | 2021-10-25 12:58:45 |
| tl_DepthOfCoverage | tool | java -jar /usr/GenomeAnalysisTK.jar -T DepthOfCoverage | broadinstitute/gatk3:3.8-1 | 2021-10-25 12:58:44 |
| tl_DepthOfCoverage4 | tool | gatk DepthOfCoverage | broadinstitute/gatk:latest | 2021-10-25 14:07:38 |
| tl_DropletUtils | tool | R function | NA | 2021-10-25 12:58:45 |
| tl_echo | tool | echo | NA | 2021-10-25 12:58:46 |
| tl_fastdump | tool | fastq-dump | quay.io/biocontainers/sra-tools:2.11.0--pl5321h314213e_2 | 2022-02-16 11:36:10 |
| tl_fastqc | tool | fastqc | hubentu/rcwl-rnaseq | 2021-10-25 12:58:46 |
| tl_featureCounts | tool | featureCounts | quay.io/biocontainers/subread:2.0.1--h7132678_2 | 2022-07-26 00:24:59 |
| tl_FilterMutectCalls | tool | gatk FilterMutectCalls | broadinstitute/gatk:latest | 2021-10-25 14:07:38 |
| tl_FilterOBias | tool | gatk FilterByOrientationBias | broadinstitute/gatk:latest | 2021-10-25 12:58:45 |
| tl_fpaste | tool | paste | NA | 2021-10-25 12:58:46 |
| tl_Funcotator | tool | gatk Funcotator | broadinstitute/gatk:latest | 2021-10-25 12:58:45 |
| tl_gc_wiggle | tool | sequenza-utils gc_wiggle | quay.io/biocontainers/sequenza-utils:3.0.0--py39h67e14b5_5 | 2022-06-16 17:40:40 |
| tl_geneBody_coverage | tool | geneBody_coverage.py | hubentu/rcwl-rnaseq | 2021-10-25 12:58:46 |
| tl_genePredToBed | tool | genePredToBed | quay.io/biocontainers/ucsc-genepredtobed:377--h0b8a92a_4 | 2021-10-25 14:07:38 |
| tl_GenomicsDB | tool | gatk GenomicsDBImport | broadinstitute/gatk:latest | 2021-10-25 14:07:38 |
| tl_GenotypeGVCFs | tool | gatk GenotypeGVCFs | broadinstitute/gatk:latest | 2021-10-25 12:58:45 |
| tl_GetPileupSummaries | tool | gatk GetPileupSummaries | broadinstitute/gatk:latest | 2021-10-25 14:07:38 |
| tl_ggsashimi | tool | guigolab/ggsashimi | 2021-10-25 12:58:46 | |
| tl_glnexus_cli_list | tool | glnexus_cli | ghcr.io/dnanexus-rnd/glnexus:v1.4.1 | 2022-06-16 17:40:40 |
| tl_glnexus_cli | tool | glnexus_cli | ghcr.io/dnanexus-rnd/glnexus:v1.4.1 | 2022-04-01 12:09:51 |
| tl_gridss | tool | gridss | quay.io/biocontainers/gridss:2.13.2--h20b1175_1 | 2022-06-16 17:40:40 |
| tl_gtf2bed | tool | bash script.sh | quay.io/biocontainers/bedops:2.4.39--h7d875b9_1 | 2021-10-25 14:07:38 |
| tl_gtfToGenePred | tool | gtfToGenePred | quay.io/biocontainers/ucsc-gtftogenepred:377--h0b8a92a_4 | 2021-10-25 14:07:38 |
| tl_HaplotypeCaller | tool | gatk HaplotypeCaller | broadinstitute/gatk:latest | 2021-10-25 12:58:45 |
| tl_hisat2_align | tool | hisat2 | biocontainers/hisat2:v2.0.5-1-deb_cv1 | 2021-10-25 12:58:46 |
| tl_hisat2_build | tool | hisat2-build | biocontainers/hisat2:v2.0.5-1-deb_cv1 | 2021-10-25 12:58:46 |
| tl_htseq | tool | htseq-count | genomicpariscentre/htseq | 2021-10-25 12:58:46 |
| tl_infer_experiment | tool | infer_experiment.py | quay.io/biocontainers/rseqc:4.0.0--py38h4a8c8d9_1 | 2022-07-11 23:12:29 |
| tl_kallisto_index | tool | kallisto index | zlskidmore/kallisto | 2021-10-25 12:58:46 |
| tl_kallisto_quant | tool | kallisto quant | zlskidmore/kallisto | 2021-10-25 12:58:46 |
| tl_lancet | tool | lancet | hubentu/lancet | 2021-10-25 14:07:38 |
| tl_LearnReadOrientationModel | tool | gatk LearnReadOrientationModel | broadinstitute/gatk:latest | 2021-10-25 12:58:45 |
| tl_liftOver | tool | liftOver | biowardrobe2/ucscuserapps:v358_2 | 2021-10-25 12:58:46 |
| tl_lofreq_indelqual | tool | lofreq indelqual | quay.io/biocontainers/lofreq:2.1.5--py37h916d2e8_4 | 2021-10-25 12:58:46 |
| tl_lofreq_viterbi | tool | lofreq viterbi | quay.io/biocontainers/lofreq:2.1.5--py37h916d2e8_4 | 2021-10-25 12:58:46 |
| tl_LoFreq | tool | lofreq somatic | quay.io/biocontainers/lofreq:2.1.5--py37h916d2e8_4 | 2021-10-25 12:58:45 |
| tl_lumpy_extractSplitReads_BwaMem | tool | extractSplitReads_BwaMem | quay.io/biocontainers/lumpy-sv:0.3.1--hdfd78af_3 | 2022-06-16 17:40:40 |
| tl_lumpy | tool | lumpyexpress | quay.io/biocontainers/lumpy-sv:0.3.1--hdfd78af_3 | 2022-06-16 17:40:40 |
| tl_mageck_count | tool | mageck count | quay.io/biocontainers/mageck:0.5.9.4--py38hed8969a_0 | 2021-10-25 12:58:46 |
| tl_mageck_mle | tool | mageck mle | quay.io/biocontainers/mageck:0.5.9.4--py38hed8969a_0 | 2021-10-25 12:58:46 |
| tl_mageck_pathway | tool | mageck pathway | quay.io/biocontainers/mageck:0.5.9.4--py38hed8969a_0 | 2021-10-25 12:58:46 |
| tl_mageck_test | tool | mageck test | quay.io/biocontainers/mageck:0.5.9.4--py38hed8969a_0 | 2021-10-25 12:58:46 |
| tl_makeblastdb | tool | makeblastdb | biocontainers/blast:v2.2.31_cv2 | 2021-10-25 12:58:46 |
| tl_manta | tool | configManta.py | quay.io/biocontainers/manta:1.6.0--h9ee0642_1 | 2021-10-25 14:07:38 |
| tl_markdup | tool | picard MarkDuplicates | quay.io/biocontainers/picard:2.21.1--0 | 2021-10-25 12:58:46 |
| tl_md5sum | tool | md5sum | NA | 2022-06-16 17:40:40 |
| tl_mergeBam | tool | picard MergeSamFiles | quay.io/biocontainers/picard:2.21.1--0 | 2021-10-25 12:58:46 |
| tl_MergeVcf_MMS | tool | R function | hubentu/variantcombiner | 2021-10-25 12:58:45 |
| tl_miRDeep2 | tool | miRDeep2.pl | hubentu/mirdeep2 | 2021-10-25 12:58:46 |
| tl_miRMapper | tool | mapper.pl | hubentu/mirdeep2 | 2021-10-25 12:58:46 |
| tl_msisensor_pro_msi | tool | msisensor-pro msi | pengjia1110/msisensor-pro | 2022-06-16 17:40:40 |
| tl_msisensor_pro_scan | tool | msisensor-pro scan | pengjia1110/msisensor-pro | 2022-06-16 17:40:40 |
| tl_multiqc | tool | multiqc | quay.io/biocontainers/multiqc:1.11--pyhdfd78af_0 | 2021-10-25 14:07:38 |
| tl_MuSE | tool | MuSE call | quay.io/biocontainers/muse:1.0.rc--h2e03b76_5 | 2021-10-25 14:07:38 |
| tl_MuSEv2 | tool | MuSE call | quay.io/biocontainers/muse:1.0.rc--0 | 2021-10-25 14:07:38 |
| tl_Mutect2_gatk3 | tool | java -jar /usr/GenomeAnalysisTK.jar -T MuTect2 | broadinstitute/gatk3:3.8-1 | 2021-10-25 12:58:45 |
| tl_Mutect2 | tool | gatk Mutect2 | broadinstitute/gatk:latest | 2021-10-25 14:07:38 |
| tl_MutSigCV | tool | gp_MutSigCV | genepattern/docker-mutsigcv:2a | 2022-07-12 12:36:23 |
| tl_mv | tool | mv | NA | 2021-10-25 14:07:38 |
| tl_mvOut | tool | R function | NA | 2021-10-25 12:58:46 |
| tl_neusomatic_call | tool | python /opt/neusomatic/neusomatic/python/call.py | msahraeian/neusomatic | 2021-10-25 12:58:46 |
| tl_neusomatic_postprocess | tool | python /opt/neusomatic/neusomatic/python/postprocess.py | msahraeian/neusomatic | 2021-10-25 12:58:46 |
| tl_neusomatic_preprocess | tool | python /opt/neusomatic/neusomatic/python/preprocess.py | msahraeian/neusomatic | 2021-10-25 12:58:46 |
| tl_Nirvana_download | tool | dotnet /opt/nirvana/Downloader.dll | annotation/nirvana:3.14 | 2023-01-05 14:49:29 |
| tl_Nirvana | tool | dotnet /opt/nirvana/Nirvana.dll | annotation/nirvana:3.14 | 2023-01-05 14:45:14 |
| tl_octopus_somatic | tool | octopus | dancooke/octopus | 2021-10-25 14:07:38 |
| tl_polysolver | tool | bash /home/polysolver/scripts/shell_call_hla_type | sachet/polysolver:v4 | 2021-10-25 12:58:46 |
| tl_PoN | tool | gatk CreateSomaticPanelOfNormals | broadinstitute/gatk:latest | 2021-10-25 14:07:38 |
| tl_pvacseq | tool | pvacseq run | griffithlab/pvactools | 2021-10-25 12:58:46 |
| tl_rbamCoverage | tool | R function | NA | 2023-01-03 16:43:10 |
| tl_read_distribution | tool | read_distribution.py | quay.io/biocontainers/rseqc:4.0.0--py38h4a8c8d9_1 | 2021-10-25 14:07:38 |
| tl_ReadBackedPhasing | tool | java -jar /usr/GenomeAnalysisTK.jar -T ReadBackedPhasing | broadinstitute/gatk3:3.8-1 | 2021-10-25 12:58:45 |
| tl_RenameSampleInVcf | tool | picard RenameSampleInVcf | quay.io/biocontainers/picard:2.21.1--0 | 2021-10-25 12:58:45 |
| tl_ReorderSam | tool | picard ReorderSam | quay.io/biocontainers/picard:2.21.1--0 | 2021-10-25 12:58:45 |
| tl_rMATS_bam | tool | xinglab/rmats | 2022-06-16 17:40:40 | |
| tl_rMATS_fq | tool | xinglab/rmats | 2022-02-16 11:36:10 | |
| tl_rMATS | tool | xinglab/rmats | 2022-02-16 11:36:10 | |
| tl_Rsplit | tool | R function | NA | 2021-10-25 12:58:45 |
| tl_runWDL | tool | java | NA | 2021-10-25 12:58:46 |
| tl_salmon_index | tool | salmon index | combinelab/salmon | 2021-10-25 12:58:46 |
| tl_salmon_quant | tool | salmon quant | combinelab/salmon | 2022-02-16 11:36:10 |
| tl_sam2bam | tool | samtools view | biocontainers/samtools:v1.7.0_cv3 | 2021-10-25 12:58:46 |
| tl_SamToFastq | tool | picard SamToFastq | quay.io/biocontainers/picard:2.21.1--0 | 2021-10-25 12:58:45 |
| tl_samtools_depth | tool | samtools depth | biocontainers/samtools:v1.7.0_cv3 | 2021-10-25 12:58:46 |
| tl_samtools_faidx | tool | samtools faidx | quay.io/biocontainers/samtools:1.15--h1170115_1 | 2022-07-25 23:36:54 |
| tl_samtools_flagstat | tool | samtools flagstat | quay.io/biocontainers/samtools:1.15--h1170115_1 | 2022-06-16 17:40:40 |
| tl_samtools_index | tool | samtools index | quay.io/biocontainers/samtools:1.12--h9aed4be_1 | 2021-10-25 12:58:46 |
| tl_samtools_merge | tool | samtools merge | quay.io/biocontainers/samtools:1.12--h9aed4be_1 | 2021-10-25 14:07:38 |
| tl_samtools_mpileup | tool | samtools mpileup | biocontainers/samtools:v1.7.0_cv3 | 2021-10-25 12:58:46 |
| tl_samtools_sort | tool | samtools sort | quay.io/biocontainers/samtools:1.12--h9aed4be_1 | 2022-02-16 11:36:10 |
| tl_samtools_stats | tool | samtools stats | biocontainers/samtools:v1.7.0_cv3 | 2021-10-25 12:58:46 |
| tl_samtools_view | tool | samtools view | quay.io/biocontainers/samtools:1.12--h9aed4be_1 | 2022-06-16 17:40:40 |
| tl_scar_HRD | tool | R function | NA | 2022-06-16 17:40:40 |
| tl_seqz_binning | tool | sequenza-utils seqz_binning | quay.io/biocontainers/sequenza-utils:3.0.0--py39h67e14b5_5 | 2022-06-16 17:40:40 |
| tl_sigproSS | tool | python /usr/local/bin/spss.py | hubentu/sigpro:v2 | 2022-08-10 16:51:24 |
| tl_somatic_combiner | tool | hubentu/somatic_combiner | 2021-10-25 14:07:38 | |
| tl_SomaticSeq_Wrapper | tool | /opt/somaticseq/SomaticSeq.Wrapper.sh | lethalfang/somaticseq:2.7.2 | 2021-10-25 14:07:38 |
| tl_SomaticSniper | tool | /opt/somatic-sniper/build/bin/bam-somaticsniper | lethalfang/somaticsniper:1.0.5.0-2 | 2021-10-25 12:58:45 |
| tl_sortBam | tool | samtools sort | biocontainers/samtools:v1.7.0_cv3 | 2021-11-22 13:13:49 |
| tl_SortVcf | tool | java -jar /usr/picard/picard.jar SortVcf | broadinstitute/picard | 2021-10-25 12:58:45 |
| tl_STAR_FFPE | tool | STAR | quay.io/biocontainers/star:2.7.9a--h9ee0642_0 | 2022-02-16 11:36:10 |
| tl_STAR_rMATS | tool | STAR | quay.io/biocontainers/star:2.7.9a--h9ee0642_0 | 2022-02-16 11:36:10 |
| tl_STAR | tool | STAR | quay.io/biocontainers/star:2.7.9a--h9ee0642_0 | 2021-10-25 14:07:38 |
| tl_starFusion | tool | /usr/local/src/STAR-Fusion/STAR-Fusion | trinityctat/ctatfusion | 2021-10-25 12:58:46 |
| tl_STARindex | tool | STAR | quay.io/biocontainers/star:2.7.10a--h9ee0642_0 | 2022-07-27 11:06:12 |
| tl_STARsolo | tool | STAR | quay.io/biocontainers/star:2.7.10a--h9ee0642_0 | 2022-07-27 11:06:12 |
| tl_strelka | tool | configureStrelkaSomaticWorkflow.py | quay.io/biocontainers/strelka:2.9.10--h9ee0642_1 | 2021-10-25 14:07:38 |
| tl_SUPPA_diffSplice | tool | python /opt/SUPPA/suppa.py diffSplice | hubentu/suppa | 2021-10-25 12:58:45 |
| tl_SUPPA_generateEvents | tool | python /opt/SUPPA/suppa.py generateEvents | hubentu/suppa | 2021-10-25 12:58:45 |
| tl_SUPPA_multipleFieldSelection | tool | python /opt/SUPPA/multipleFieldSelection.py | hubentu/suppa | 2021-10-25 12:58:45 |
| tl_SUPPA_psiPerEvent | tool | python /opt/SUPPA/suppa.py psiPerEvent | hubentu/suppa | 2021-10-25 12:58:45 |
| tl_svaba_germline | tool | svaba run | quay.io/biocontainers/svaba:1.1.0--h7d7f7ad_2 | 2022-06-16 17:40:40 |
| tl_svaba_somatic | tool | svaba run | quay.io/biocontainers/svaba:1.1.0--h7d7f7ad_2 | 2021-10-25 14:07:38 |
| tl_SVE_VP | tool | /software/SVE/scripts/variant_processor.py | timothyjamesbecker/sve | 2021-10-25 12:58:45 |
| tl_SVE | tool | /software/SVE/scripts/auto.py | timothyjamesbecker/sve | 2021-10-25 12:58:45 |
| tl_tabix_index | tool | tabix | biocontainers/tabix:v1.3.2-2-deb_cv1 | 2021-10-25 12:58:46 |
| tl_tar_c | tool | tar | NA | 2022-06-16 17:40:40 |
| tl_trim_galore | tool | trim_galore | quay.io/biocontainers/trim-galore:0.6.7--hdfd78af_0 | 2022-06-16 17:40:40 |
| tl_VarDict | tool | vardict-java | quay.io/biocontainers/vardict-java:1.8.2--hdfd78af_1 | 2021-10-25 12:58:45 |
| tl_VarScan2_processSomatic | tool | java -jar /opt/varscan/VarScan.jar processSomatic | mgibio/varscan-cwl:v2.4.2-samtools1.3.1 | 2021-10-25 12:58:45 |
| tl_VarScan2_somatic | tool | java -jar /opt/varscan/VarScan.jar somatic | mgibio/varscan-cwl:v2.4.2-samtools1.3.1 | 2021-10-25 12:58:45 |
| tl_VarScan2_somaticFilter | tool | java -jar /opt/varscan/VarScan.jar somaticFilter | mgibio/varscan-cwl:v2.4.2-samtools1.3.1 | 2021-10-25 12:58:45 |
| tl_VarScan2 | tool | serge2016/varscan:v0.1.1 | 2021-10-25 12:58:45 | |
| tl_vcf_expression_annotator | tool | vcf-expression-annotator | griffithlab/vatools:3.1.0 | 2021-10-25 12:58:46 |
| tl_vcf_readcount_annotator | tool | vcf-readcount-annotator | griffithlab/vatools:3.1.0 | 2021-10-25 12:58:46 |
| tl_vcf2bed | tool | bash script.sh | quay.io/biocontainers/bedtools:2.30.0--h7d7f7ad_2 | 2021-10-25 14:07:38 |
| tl_vep_plugin | tool | vep | hubentu/ensembl-vep-plugins | 2021-10-25 14:07:38 |
| tl_vep | tool | vep | ensemblorg/ensembl-vep | 2022-02-16 11:36:10 |
| tl_vt_decompose | tool | vt decompose | hubentu/vt | 2021-10-25 12:58:46 |
← bwaMMRecal BaseRecal →