Merge pull request #76 from fulaibaowang/reports_fraser_mae

Reports fraser mae

Author: fulaibaowang

assets/multiqc_config.yml

@@ -2,6 +2,7 @@ report_comment: >
   This report has been generated by the <a href="https://github.com/nf-core/drop/tree/dev" target="_blank">nf-core/drop</a>
   analysis pipeline. For information about how to interpret these results, please see the
   <a href="https://nf-co.re/drop/dev/docs/output" target="_blank">documentation</a>.
+
 report_section_order:
   "nf-core-drop-methods-description":
     order: -1000

assets/multiqc_configs/multiqc_fraser_config.yml

@@ -0,0 +1,70 @@
+custom_content:
+  order:
+    - fraser_overview
+    - q_estimation_psi5
+    - q_estimation_psi3
+    - q_estimation_theta
+    - q_estimation_jaccard
+    - aberrantly_spliced_genes
+    - batch_correlation_psi5_FALSE
+    - batch_correlation_psi5_TRUE
+    - batch_correlation_psi3_FALSE
+    - batch_correlation_psi3_TRUE
+    - batch_correlation_theta_FALSE
+    - batch_correlation_theta_TRUE
+    - batch_correlation_jaccard_FALSE
+    - batch_correlation_jaccard_TRUE
+    - total_outliers
+    - results
+
+custom_data:
+  fraser_overview:
+    section_name: "Fraser overview"
+    format: "tsv"
+    plot_type: "table"
+
+  q_estimation_psi5:
+    section_name: "Hyperparameter optimization - Q_estimation_psi5"
+
+  q_estimation_psi3:
+    section_name: "Hyperparameter optimization - Q_estimation_psi3"
+
+  q_estimation_theta:
+    section_name: "Hyperparameter optimization - Q_estimation_theta"
+
+  q_estimation_jaccard:
+    section_name: "Hyperparameter optimization"
+    description: "Q_estimation_jaccard"
+
+  aberrantly_spliced_genes:
+    section_name: "Aberrantly spliced genes"
+
+  batch_correlation_psi5_FALSE:
+    section_name: "Batch Correlation psi5 raw"
+  batch_correlation_psi5_TRUE:
+    section_name: "Batch correlation psi5 normalized"
+
+  batch_correlation_psi3_FALSE:
+    section_name: "Batch Correlation psi3 raw"
+  batch_correlation_psi3_TRUE:
+    section_name: "Batch correlation psi3 normalized"
+
+  batch_correlation_theta_FALSE:
+    section_name: "Batch Correlation theta raw"
+  batch_correlation_theta_TRUE:
+    section_name: "Batch correlation theta normalized"
+
+  batch_correlation_jaccard_FALSE:
+    section_name: "Batch Correlation jaccard raw"
+  batch_correlation_jaccard_TRUE:
+    section_name: "Batch correlation jaccard normalized"
+
+  total_outliers:
+    section_name: "Results"
+    format: "tsv"
+    plot_type: "table"
+    description: "Total splicing outliers"
+
+  results:
+    section_name: "Results table"
+    description: "FRASER results (up to 500 rows shown)"

assets/multiqc_countexpression_config.yml renamed to assets/multiqc_configs/multiqc_genecounts_config.yml

@@ -0,0 +1,36 @@
+custom_content:
+  order:
+    - mae_overview
+    - cascade_plot
+    - variant_frequency
+    - median_of_each_category
+    - results
+
+custom_data:
+  mae_overview:
+    section_name: "MAE overview"
+    format: "tsv"
+    plot_type: "table"
+
+  cascade_plot:
+    section_name: "Cascade plot"
+    description: |
+      a cascade plot that shows a progression of added filters
+
+      - `>10 counts`: only variants supported by more than 10 counts
+      - `+MAE`: and shows mono allelic expression
+      - `+MAE for REF`: the monoallelic expression favors the reference allele
+      - `+MAE for ALT`: the monoallelic expression favors the alternative allele
+      - `rare`:
+        - if add_AF is set to true in config file must meet minimum AF set by the config value max_AF
+        - must meet the inner-cohort frequency maxVarFreqCohort cutoff
+
+  variant_frequency:
+    section_name: "Variant Frequency within Cohort"
+
+  median_of_each_category:
+    section_name: "Median of each category"
+
+  results:
+    section_name: "MAE Results table"
+    description: "MAE results (up to 500 rows shown)"

assets/multiqc_configs/multiqc_mae_config.yml

@@ -0,0 +1,42 @@
+custom_content:
+  order:
+    - matching_values_distribution
+    - heatmap_matching_variants
+    - identify_matching_samples
+    - false_matches
+    - false_mismatches
+
+custom_data:
+  matching_values_distribution:
+    section_name: "DNA - RNA matching values distribution"
+
+  heatmap_matching_variants:
+    section_name: "Heatmap of matching variants"
+    description: |
+      Shows the proportion of matching DNA (rows) - RNA (cols) variants. Possible values are:
+
+      - match: the DNA sample matches the annotated RNA sample
+      - no match: the DNA sample does not match the annotated RNA and no match was found
+      - matches other: the DNA sample does not match the annotated RNA, but another match was found
+      - matches more: the DNA sample matches the annotated RNA, but also other RNAs not annotated to match
+      - matches less: the DNA sample is annotated with more than 1 RNA. Not all annotated RNAs are correct.
+
+      Similar for the RNAs.
+
+  identify_matching_samples:
+    section_name: "Identify matching samples"
+    format: "tsv"
+    plot_type: "table"
+    description: |
+      Considerations: On our experience, the median of the proportion of matching variants in matching samples is around 0.95, and the median of the proportion of matching variants in not matching samples is around 0.58. Sometimes we do see some values between 0.7 - 0.85. That could mean that the DNA-RNA combination is not from the same person, but from a relative. It could also be due to a technical error. For those cases, check the following:
+
+      - RNA sequencing depth (low seq depth that can lead to variants not to be found in the RNA)
+      - Number of variants (too many variants called due to sequencing errors)
+      - Ratio of heterozygous/homozygous variants (usually too many called variants means too many heterozygous ones)
+      - Is the sample a relative of the other?
+
+  false_matches:
+    section_name: "Samples that were annotated to match but do not"
+
+  false_mismatches:
+    section_name: "Samples that were not annotated to match but actually do"

assets/multiqc_configs/multiqc_maeqc_config.yml

@@ -0,0 +1,45 @@
+custom_content:
+  order:
+    - number_of_samples
+    - number_of_introns
+    - number_of_splice_sites
+    - comparison_local_and_external
+    - expression_filtering
+
+custom_data:
+  number_of_samples:
+    section_name: "Number of samples"
+    format: "tsv"
+    plot_type: "table"
+
+  number_of_introns:
+    section_name: "Number of introns"
+    format: "tsv"
+    plot_type: "table"
+
+  number_of_splice_sites:
+    section_name: "Number of splice sites"
+    format: "tsv"
+    plot_type: "table"
+
+  comparison_local_and_external:
+    section_name: "Comparison of local and external counts"
+    description: |
+      Using external counts
+
+      External counts introduce some complexity into the problem of counting junctions because it is unknown whether or not a junction is not counted (because there are no reads) compared to filtered and not present due to legal/personal sharing reasons. As a result, after merging the local (counted from BAM files) counts and the external counts, only the junctions that are present in both remain. As a result it is likely that the number of junctions will decrease after merging.
+
+  expression_filtering:
+    section_name: "Expression filtering"
+    description: |
+      The expression filtering step removes introns that are lowly expressed. The requirements for an intron to pass this filter are:
+
+      - at least 1 sample has 20 counts (K) for the intron
+      - at least 5% of the samples need to have a total of at least 10 reads for the splice metric denominator (N) of the intron
+
+  variability_filtering:
+    section_name: "Variability filtering"
+    description: |
+      The variability filtering step removes introns that have no or little variability in the splice metric values across samples. The requirement for an intron to pass this filter is:
+
+      - at least 1 sample has a difference of at least 0.05 in the splice metric compared to the mean splice metric of the intron

assets/multiqc_outrider_config.yml renamed to assets/multiqc_configs/multiqc_outrider_config.yml

@@ -299,6 +299,7 @@ process {
         ext.prefix = { meta.annotation }
         publishDir = [
             path: { "${params.outdir}/processed_results/mae/${meta.drop_group}" },
+            pattern: "MAE_results_*",
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
             overwrite: true
@@ -332,49 +333,139 @@ process {
     //
     // Other processes
     //
-    withName: 'MULTIQC_COUNTEXPRESSION' {
+    withName: 'DROP.*MULTIQC_GENECOUNTS' {
         publishDir = [
             path: { "${params.outdir}/reports/aberrant_expression/genecounts" },
             mode: params.publish_dir_mode,
-            saveAs: {
-                filename ->
-                    switch (filename) {
-                        case 'versions.yml':
-                            null
-                            break
-                        case ~/\[TAG:.+\]_multiqc_(report\.html|plots|data)/:
-                            def tag = (filename =~ /\[TAG:(.+)\]_multiqc_(report\.html|plots|data)/)[0][1]
-                            def new_filename = filename.replaceFirst(
-                                "(?<prefix>.*)\\[TAG:${tag}\\]_(?<suffix>multiqc_(report\\.html|plots|data).*)",
-                                '${prefix}${suffix}')
-                            "${tag}/${new_filename}"
-                            break
-                        default:
-                            filename
+            saveAs: { filename ->
+                if (filename == 'versions.yml') {
+                    return null
+                }
+                else if (filename ==~ /\[TAG:genecounts_.+\]_multiqc_(report_mqc\.html|plots|data)/) {
+                    def tag = (filename =~ /\[TAG:genecounts_(.+)\]_multiqc_(report_mqc\.html|plots|data)/)[0][1]
+                    def new_filename = filename.replaceFirst(
+                        "(?<prefix>.*)\\[TAG:genecounts_${tag}\\]_(?<suffix>multiqc_(report_mqc\\.html|plots|data).*)",
+                        '${prefix}${suffix}'
+                    )
+                    return "${tag}/${new_filename}"
+                }
+                else {
+                    return filename
                 }
             }
         ]
     }
 
-    withName: 'MULTIQC_OUTRIDER' {
+    withName: 'DROP.*MULTIQC_OUTRIDER' {
         publishDir = [
             path: { "${params.outdir}/reports/aberrant_expression/outrider" },
             mode: params.publish_dir_mode,
-            saveAs: {
-                filename ->
-                    switch (filename) {
-                        case 'versions.yml':
-                            null
-                            break
-                        case ~/\[TAG:.+\]_multiqc_(report\.html|plots|data)/:
-                            def tag = (filename =~ /\[TAG:(.+)\]_multiqc_(report\.html|plots|data)/)[0][1]
-                            def new_filename = filename.replaceFirst(
-                                "(?<prefix>.*)\\[TAG:${tag}\\]_(?<suffix>multiqc_(report\\.html|plots|data).*)",
-                                '${prefix}${suffix}')
-                            "${tag}/${new_filename}"
-                            break
-                        default:
-                            filename
+            saveAs: { filename ->
+                if (filename == 'versions.yml') {
+                    return null
+                }
+                else if (filename ==~ /\[TAG:outrider_.+\]_multiqc_(report_mqc\.html|plots|data)/) {
+                    def tag = (filename =~ /\[TAG:outrider_(.+)\]_multiqc_(report_mqc\.html|plots|data)/)[0][1]
+                    def new_filename = filename.replaceFirst(
+                        "(?<prefix>.*)\\[TAG:outrider_${tag}\\]_(?<suffix>multiqc_(report_mqc\\.html|plots|data).*)",
+                        '${prefix}${suffix}'
+                    )
+                    return "${tag}/${new_filename}"
+                }
+                else {
+                    return filename
+                }
+            }
+        ]
+    }
+
+    withName: 'DROP.*MULTIQC_SPLICECOUNTS' {
+        publishDir = [
+            path: { "${params.outdir}/reports/aberrant_splicing/splicecounts" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename ->
+                if (filename == 'versions.yml') {
+                    return null
+                }
+                else if (filename ==~ /\[TAG:splicecounts_.+\]_multiqc_(report_mqc\.html|plots|data)/) {
+                    def tag = (filename =~ /\[TAG:splicecounts_(.+)\]_multiqc_(report_mqc\.html|plots|data)/)[0][1]
+                    def new_filename = filename.replaceFirst(
+                        "(?<prefix>.*)\\[TAG:splicecounts_${tag}\\]_(?<suffix>multiqc_(report_mqc\\.html|plots|data).*)",
+                        '${prefix}${suffix}'
+                    )
+                    return "${tag}/${new_filename}"
+                }
+                else {
+                    return filename
+                }
+            }
+        ]
+    }
+
+    withName: 'DROP.*MULTIQC_FRASER' {
+        publishDir = [
+            path: { "${params.outdir}/reports/aberrant_splicing/fraser" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename ->
+                if (filename == 'versions.yml') {
+                    return null
+                }
+                else if (filename ==~ /\[TAG:fraser_.+\]_multiqc_(report_mqc\.html|plots|data)/) {
+                    def tag = (filename =~ /\[TAG:fraser_(.+)\]_multiqc_(report_mqc\.html|plots|data)/)[0][1]
+                    def new_filename = filename.replaceFirst(
+                        "(?<prefix>.*)\\[TAG:fraser_${tag}\\]_(?<suffix>multiqc_(report_mqc\\.html|plots|data).*)",
+                        '${prefix}${suffix}'
+                    )
+                    return "${tag}/${new_filename}"
+                }
+                else {
+                    return filename
+                }
+            }
+        ]
+    }
+
+    withName: 'DROP.*MULTIQC_MAE' {
+        publishDir = [
+            path: { "${params.outdir}/reports/mae/mae" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename ->
+                if (filename == 'versions.yml') {
+                    return null
+                }
+                else if (filename ==~ /\[TAG:mae_.+\]_multiqc_(report_mqc\.html|plots|data)/) {
+                    def tag = (filename =~ /\[TAG:mae_(.+)\]_multiqc_(report_mqc\.html|plots|data)/)[0][1]
+                    def new_filename = filename.replaceFirst(
+                        "(?<prefix>.*)\\[TAG:mae_${tag}\\]_(?<suffix>multiqc_(report_mqc\\.html|plots|data).*)",
+                        '${prefix}${suffix}'
+                    )
+                    return "${tag}/${new_filename}"
+                }
+                else {
+                    return filename
+                }
+            }
+        ]
+    }
+
+    withName: 'DROP.*MULTIQC_MAEQC' {
+        publishDir = [
+            path: { "${params.outdir}/reports/mae/maeqc" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename ->
+                if (filename == 'versions.yml') {
+                    return null
+                }
+                else if (filename ==~ /\[TAG:maeqc_.+\]_multiqc_(report_mqc\.html|plots|data)/) {
+                    def tag = (filename =~ /\[TAG:maeqc_(.+)\]_multiqc_(report_mqc\.html|plots|data)/)[0][1]
+                    def new_filename = filename.replaceFirst(
+                        "(?<prefix>.*)\\[TAG:maeqc_${tag}\\]_(?<suffix>multiqc_(report_mqc\\.html|plots|data).*)",
+                        '${prefix}${suffix}'
+                    )
+                    return "${tag}/${new_filename}"
+                }
+                else {
+                    return filename
                 }
             }
         ]
@@ -389,5 +480,4 @@ process {
         ]
     }
 
-
 }