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maxulysse

code polish

Jan 23, 2025

2ecf58f · Jan 23, 2025

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Name		Name	Last commit message	Last commit date
parent directory ..
annotation_cache_initialisation		annotation_cache_initialisation	Retiring snpeff_genome. (Just using snpeff_db.)	Sep 18, 2024
bam_applybqsr		bam_applybqsr	fix channels' meta for preprocessing	Apr 8, 2024
bam_applybqsr_spark		bam_applybqsr_spark	fix channels' meta for preprocessing	Apr 8, 2024
bam_baserecalibrator		bam_baserecalibrator	no it	Jan 23, 2025
bam_baserecalibrator_spark		bam_baserecalibrator_spark	fix channels' meta for preprocessing	Apr 8, 2024
bam_convert_samtools		bam_convert_samtools	indent things, clean up, add comments, consolidate	Jul 10, 2023
bam_joint_calling_germline_gatk		bam_joint_calling_germline_gatk	fix usage of GATK4_GENOTYPEGVCFS	Sep 24, 2024
bam_joint_calling_germline_sentieon		bam_joint_calling_germline_sentieon	fix various sentieon module calls	Dec 9, 2024
bam_markduplicates		bam_markduplicates	fix channels' meta for preprocessing	Apr 8, 2024
bam_markduplicates_spark		bam_markduplicates_spark	fix channels	Apr 9, 2024
bam_merge_index_samtools		bam_merge_index_samtools	clean up	Jun 2, 2023
bam_sentieon_dedup		bam_sentieon_dedup	Fixing fasta and fai channels for call to SENTIEON_DEDUP	Apr 15, 2024
bam_variant_calling_cnvkit		bam_variant_calling_cnvkit	fix linting	Aug 5, 2024
bam_variant_calling_deepvariant		bam_variant_calling_deepvariant	fix a couple tests	Sep 23, 2024
bam_variant_calling_freebayes		bam_variant_calling_freebayes	update channels' meta	Apr 8, 2024
bam_variant_calling_germline_all		bam_variant_calling_germline_all	fix channel name	Dec 10, 2024
bam_variant_calling_germline_manta		bam_variant_calling_germline_manta	fix channels for manta	Nov 1, 2023
bam_variant_calling_haplotypecaller		bam_variant_calling_haplotypecaller	Removing meta in certain input-channels in call to GATK4_HAPLOTYPECALLER	Feb 23, 2024
bam_variant_calling_indexcov		bam_variant_calling_indexcov	fix channel name	Dec 10, 2024
bam_variant_calling_mpileup		bam_variant_calling_mpileup	update channels' meta	Apr 8, 2024
bam_variant_calling_sentieon_dnascope		bam_variant_calling_sentieon_dnascope	Fixing fasta and fai input channels in Sentieon workflows	Apr 17, 2024
bam_variant_calling_sentieon_haplotyper		bam_variant_calling_sentieon_haplotyper	fix various sentieon module calls	Dec 9, 2024
bam_variant_calling_single_strelka		bam_variant_calling_single_strelka	indent things, clean up, add comments, consolidate	Jul 10, 2023
bam_variant_calling_single_tiddit		bam_variant_calling_single_tiddit	indent things, clean up, add comments, consolidate	Jul 10, 2023
bam_variant_calling_somatic_all		bam_variant_calling_somatic_all	fix channel name	Dec 10, 2024
bam_variant_calling_somatic_ascat		bam_variant_calling_somatic_ascat	simplify ascat usage	Dec 19, 2023
bam_variant_calling_somatic_controlfreec		bam_variant_calling_somatic_controlfreec	Removed extra space	Feb 23, 2024
bam_variant_calling_somatic_manta		bam_variant_calling_somatic_manta	fix channels for manta	Nov 1, 2023
bam_variant_calling_somatic_mutect2		bam_variant_calling_somatic_mutect2	Update subworkflows/local/bam_variant_calling_somatic_mutect2/main.nf	Nov 3, 2023
bam_variant_calling_somatic_strelka		bam_variant_calling_somatic_strelka	indent things, clean up, add comments, consolidate	Jul 10, 2023
bam_variant_calling_somatic_tiddit		bam_variant_calling_somatic_tiddit	sort inputs	Oct 25, 2024
bam_variant_calling_tumor_only_all		bam_variant_calling_tumor_only_all	Remove Strelka tumor-only somatic variant calling (#1709)	Oct 29, 2024
bam_variant_calling_tumor_only_controlfreec		bam_variant_calling_tumor_only_controlfreec	Updated makegraph to makegraph2	Feb 15, 2024
bam_variant_calling_tumor_only_lofreq		bam_variant_calling_tumor_only_lofreq	Update main.nf	Aug 29, 2024
bam_variant_calling_tumor_only_manta		bam_variant_calling_tumor_only_manta	fix channels for manta	Nov 1, 2023
bam_variant_calling_tumor_only_mutect2		bam_variant_calling_tumor_only_mutect2	code polish	Apr 9, 2024
channel_align_create_csv		channel_align_create_csv	remove params from CHANNEL_*_CSV subworkflows	Dec 19, 2023
channel_applybqsr_create_csv		channel_applybqsr_create_csv	remove params from CHANNEL_*_CSV subworkflows	Dec 19, 2023
channel_baserecalibrator_create_csv		channel_baserecalibrator_create_csv	remove params from CHANNEL_*_CSV subworkflows	Dec 19, 2023
channel_markduplicates_create_csv		channel_markduplicates_create_csv	remove params from CHANNEL_*_CSV subworkflows	Dec 19, 2023
channel_variant_calling_create_csv		channel_variant_calling_create_csv	remove params from CHANNEL_*_CSV subworkflows	Dec 19, 2023
cram_merge_index_samtools		cram_merge_index_samtools	fix cram_merge_index_samtools	May 24, 2023
cram_qc_mosdepth_samtools		cram_qc_mosdepth_samtools	Update subworkflows/local/cram_qc_mosdepth_samtools/main.nf	Apr 9, 2024
cram_sampleqc		cram_sampleqc	fix channels' meta for preprocessing	Apr 8, 2024
download_cache_snpeff_vep		download_cache_snpeff_vep	move annotation cache logic in its own subworkflow	Oct 30, 2023
fastq_align_bwamem_mem2_dragmap_sentieon		fastq_align_bwamem_mem2_dragmap_sentieon	fix channels' meta for preprocessing	Apr 8, 2024
fastq_create_umi_consensus_fgbio		fastq_create_umi_consensus_fgbio	Fix default value	Sep 24, 2024
post_variantcalling		post_variantcalling	code polish	Dec 19, 2023
prepare_genome		prepare_genome	collect	Apr 9, 2024
prepare_intervals		prepare_intervals	code polish	Jan 23, 2025
prepare_reference_cnvkit		prepare_reference_cnvkit	fix channels cardinality	Apr 9, 2024
samplesheet_to_channel		samplesheet_to_channel	rescue more comments	Jan 23, 2025
utils_nfcore_sarek_pipeline		utils_nfcore_sarek_pipeline	Fix bug where workflow can hang if the email parameter is set.	Dec 6, 2024
vcf_annotate_all		vcf_annotate_all	fix(channels): fix remapping of channels	Apr 18, 2024
vcf_annotate_bcftools		vcf_annotate_bcftools	typo	Sep 23, 2024
vcf_concatenate_germline		vcf_concatenate_germline	fix import paths	Jul 10, 2023
vcf_qc_bcftools_vcftools		vcf_qc_bcftools_vcftools	Trying to input-channels for BCFTOOLS_STATS right	Aug 15, 2023
vcf_variant_filtering_gatk		vcf_variant_filtering_gatk	Avoiding addition of variant_caller meta-tag in VCF_VARIANT_FILTERING…	May 31, 2023
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