From 283ea0590788fce44d42be99f2ac3033cc50ee90 Mon Sep 17 00:00:00 2001 From: Gabriela Carvalho Date: Mon, 19 May 2025 14:57:29 -0300 Subject: [PATCH 1/4] mv: moved nextflow to src dir --- {workflow => src}/bin/merge_files.py | 0 {workflow => src}/main.nf | 0 {modules => src/modules}/basecall.nf | 0 {modules => src/modules}/calculate_coverage.nf | 0 {modules => src/modules}/convert_input_from_minknow.nf | 0 {modules => src/modules}/filter_bam.nf | 0 {modules => src/modules}/modkit.nf | 0 {modules => src/modules}/multiqc.nf | 0 {modules => src/modules}/num_reads_report.nf | 0 {modules => src/modules}/pycoqc.nf | 0 {workflow => src}/nextflow.config | 0 {sub_workflows => src/sub_workflows}/BASECALLING.nf | 0 .../sub_workflows}/FILTERING_AND_QC_FROM_MINKNOW.nf | 0 .../sub_workflows}/FILTERING_AND_QC_FROM_STEP_1.nf | 0 {sub_workflows => src/sub_workflows}/MODKIT_AND_MULTIQC.nf | 0 15 files changed, 0 insertions(+), 0 deletions(-) rename {workflow => src}/bin/merge_files.py (100%) rename {workflow => src}/main.nf (100%) rename {modules => src/modules}/basecall.nf (100%) rename {modules => src/modules}/calculate_coverage.nf (100%) rename {modules => src/modules}/convert_input_from_minknow.nf (100%) rename {modules => src/modules}/filter_bam.nf (100%) rename {modules => src/modules}/modkit.nf (100%) rename {modules => src/modules}/multiqc.nf (100%) rename {modules => src/modules}/num_reads_report.nf (100%) rename {modules => src/modules}/pycoqc.nf (100%) rename {workflow => src}/nextflow.config (100%) rename {sub_workflows => src/sub_workflows}/BASECALLING.nf (100%) rename {sub_workflows => src/sub_workflows}/FILTERING_AND_QC_FROM_MINKNOW.nf (100%) rename {sub_workflows => src/sub_workflows}/FILTERING_AND_QC_FROM_STEP_1.nf (100%) rename {sub_workflows => src/sub_workflows}/MODKIT_AND_MULTIQC.nf (100%) diff --git a/workflow/bin/merge_files.py b/src/bin/merge_files.py similarity index 100% rename from workflow/bin/merge_files.py rename to src/bin/merge_files.py diff --git a/workflow/main.nf b/src/main.nf similarity index 100% rename from workflow/main.nf rename to src/main.nf diff --git a/modules/basecall.nf b/src/modules/basecall.nf similarity index 100% rename from modules/basecall.nf rename to src/modules/basecall.nf diff --git a/modules/calculate_coverage.nf b/src/modules/calculate_coverage.nf similarity index 100% rename from modules/calculate_coverage.nf rename to src/modules/calculate_coverage.nf diff --git a/modules/convert_input_from_minknow.nf b/src/modules/convert_input_from_minknow.nf similarity index 100% rename from modules/convert_input_from_minknow.nf rename to src/modules/convert_input_from_minknow.nf diff --git a/modules/filter_bam.nf b/src/modules/filter_bam.nf similarity index 100% rename from modules/filter_bam.nf rename to src/modules/filter_bam.nf diff --git a/modules/modkit.nf b/src/modules/modkit.nf similarity index 100% rename from modules/modkit.nf rename to src/modules/modkit.nf diff --git a/modules/multiqc.nf b/src/modules/multiqc.nf similarity index 100% rename from modules/multiqc.nf rename to src/modules/multiqc.nf diff --git a/modules/num_reads_report.nf b/src/modules/num_reads_report.nf similarity index 100% rename from modules/num_reads_report.nf rename to src/modules/num_reads_report.nf diff --git a/modules/pycoqc.nf b/src/modules/pycoqc.nf similarity index 100% rename from modules/pycoqc.nf rename to src/modules/pycoqc.nf diff --git a/workflow/nextflow.config b/src/nextflow.config similarity index 100% rename from workflow/nextflow.config rename to src/nextflow.config diff --git a/sub_workflows/BASECALLING.nf b/src/sub_workflows/BASECALLING.nf similarity index 100% rename from sub_workflows/BASECALLING.nf rename to src/sub_workflows/BASECALLING.nf diff --git a/sub_workflows/FILTERING_AND_QC_FROM_MINKNOW.nf b/src/sub_workflows/FILTERING_AND_QC_FROM_MINKNOW.nf similarity index 100% rename from sub_workflows/FILTERING_AND_QC_FROM_MINKNOW.nf rename to src/sub_workflows/FILTERING_AND_QC_FROM_MINKNOW.nf diff --git a/sub_workflows/FILTERING_AND_QC_FROM_STEP_1.nf b/src/sub_workflows/FILTERING_AND_QC_FROM_STEP_1.nf similarity index 100% rename from sub_workflows/FILTERING_AND_QC_FROM_STEP_1.nf rename to src/sub_workflows/FILTERING_AND_QC_FROM_STEP_1.nf diff --git a/sub_workflows/MODKIT_AND_MULTIQC.nf b/src/sub_workflows/MODKIT_AND_MULTIQC.nf similarity index 100% rename from sub_workflows/MODKIT_AND_MULTIQC.nf rename to src/sub_workflows/MODKIT_AND_MULTIQC.nf -- GitLab From eee1985286276f7d6f7f9ec3216729fd3bb3ddc3 Mon Sep 17 00:00:00 2001 From: Gabriela Carvalho Date: Tue, 20 May 2025 15:51:29 -0300 Subject: [PATCH 2/4] Modified project structure --- src/main.nf | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/main.nf b/src/main.nf index 6b45ca5..e0a983f 100755 --- a/src/main.nf +++ b/src/main.nf @@ -46,10 +46,10 @@ MultiQC configuration file : ${params.multiqc_config} } // Import Workflows -include {BASECALLING} from '../sub_workflows/BASECALLING' -include {FILTERING_AND_QC_FROM_STEP_1} from '../sub_workflows/FILTERING_AND_QC_FROM_STEP_1.nf' -include {FILTERING_AND_QC_FROM_MINKNOW} from '../sub_workflows/FILTERING_AND_QC_FROM_MINKNOW.nf' -include {MODKIT_AND_MULTIQC} from '../sub_workflows/MODKIT_AND_MULTIQC.nf' +include {BASECALLING} from './sub_workflows/BASECALLING' +include {FILTERING_AND_QC_FROM_STEP_1} from './sub_workflows/FILTERING_AND_QC_FROM_STEP_1.nf' +include {FILTERING_AND_QC_FROM_MINKNOW} from './sub_workflows/FILTERING_AND_QC_FROM_MINKNOW.nf' +include {MODKIT_AND_MULTIQC} from './sub_workflows/MODKIT_AND_MULTIQC.nf' // Define initial files and channels if (params.step.toString() == "1") { -- GitLab From 02cb1c42b00b6072f89cf0882ef9dc6fb9d997fd Mon Sep 17 00:00:00 2001 From: Gabriela Carvalho Date: Wed, 21 May 2025 15:46:18 -0300 Subject: [PATCH 3/4] Path change nextflow .src/main.nf --- README.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index e62a135..dd40500 100755 --- a/README.md +++ b/README.md @@ -254,7 +254,7 @@ The following examples assume your current directory is the root directory of th 1. STEP 1: GPU basecalling without demultiplexing ```sh - nextflow ./workflow/main.nf \ + nextflow .src/main.nf \ --basecall_path "$BASECALL_PATH" \ --basecall_speed "hac" \ --step 1 \ @@ -274,7 +274,7 @@ The following examples assume your current directory is the root directory of th 1. STEP 2A: Alignment Filtering and Quality Control from STEP 1 ```sh - nextflow ./workflow/main.nf \ + nextflow .src/main.nf \ --steps_2_and_3_input_directory "./results/$OUTPUT_DIR_NAME/" \ --min_mapped_reads_thresh 500 \ --qscore_thresh 9 \ @@ -286,7 +286,7 @@ The following examples assume your current directory is the root directory of th 1. STEP 2B (MinKNOW): Alignment Filtering and Quality Control from MinKNOW basecalling and alignment (bam files were generated by MinKNOW) ```sh - nextflow ./workflow/main.nf \ + nextflow .src/main.nf \ --steps_2_and_3_input_directory "./results/$OUTPUT_DIR_NAME/" \ --min_mapped_reads_thresh 500 \ --is_barcoded "True" \ @@ -299,7 +299,7 @@ The following examples assume your current directory is the root directory of th 1. STEP 3: Methylation calling and MultiQC report ```sh - nextflow ./workflow/main.nf \ + nextflow .src/main.nf \ --steps_2_and_3_input_directory "./results/$OUTPUT_DIR_NAME/" \ --multiqc_config "./references/multiqc_config.yaml" \ --step 3 \ -- GitLab From f3d78e0de49d27705f999d9ca7aa2d02d6ad3b14 Mon Sep 17 00:00:00 2001 From: Gabriela Carvalho Date: Wed, 21 May 2025 16:25:36 -0300 Subject: [PATCH 4/4] Typographical error correction .src/ to ./src/ --- README.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index dd40500..ee239bc 100755 --- a/README.md +++ b/README.md @@ -254,7 +254,7 @@ The following examples assume your current directory is the root directory of th 1. STEP 1: GPU basecalling without demultiplexing ```sh - nextflow .src/main.nf \ + nextflow ./src/main.nf \ --basecall_path "$BASECALL_PATH" \ --basecall_speed "hac" \ --step 1 \ @@ -274,7 +274,7 @@ The following examples assume your current directory is the root directory of th 1. STEP 2A: Alignment Filtering and Quality Control from STEP 1 ```sh - nextflow .src/main.nf \ + nextflow ./src/main.nf \ --steps_2_and_3_input_directory "./results/$OUTPUT_DIR_NAME/" \ --min_mapped_reads_thresh 500 \ --qscore_thresh 9 \ @@ -286,7 +286,7 @@ The following examples assume your current directory is the root directory of th 1. STEP 2B (MinKNOW): Alignment Filtering and Quality Control from MinKNOW basecalling and alignment (bam files were generated by MinKNOW) ```sh - nextflow .src/main.nf \ + nextflow ./src/main.nf \ --steps_2_and_3_input_directory "./results/$OUTPUT_DIR_NAME/" \ --min_mapped_reads_thresh 500 \ --is_barcoded "True" \ @@ -299,7 +299,7 @@ The following examples assume your current directory is the root directory of th 1. STEP 3: Methylation calling and MultiQC report ```sh - nextflow .src/main.nf \ + nextflow ./src/main.nf \ --steps_2_and_3_input_directory "./results/$OUTPUT_DIR_NAME/" \ --multiqc_config "./references/multiqc_config.yaml" \ --step 3 \ -- GitLab