diff --git a/CHANGELOG.md b/CHANGELOG.md index c33bd644..7cc0d258 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -29,6 +29,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [[#396](https://github.com/nf-core/chipseq/issues/396)] - Check that samplesheet samples IDs do only have alphanumeric characters, dots, dashes or underscores. - [[#378](https://github.com/nf-core/chipseq/issues/378)] - Switch from macs2 to macs3. - [[#347](https://github.com/nf-core/chipseq/issues/347)] - Add read group tag to bam files processed by bowtie2. +- [[PR #406](https://github.com/nf-core/chipseq/pull/406)] - Update metro map to show macs3 instead of macs2. ### Software dependencies diff --git a/docs/images/mqc_macs2_peak_count_plot.png b/docs/images/mqc_macs3_peak_count_plot.png similarity index 100% rename from docs/images/mqc_macs2_peak_count_plot.png rename to docs/images/mqc_macs3_peak_count_plot.png diff --git a/docs/images/nf-core-chipseq_metro_map_grey.png 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style="color:#000000;font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:medium;line-height:normal;font-family:sans-serif;text-indent:0;text-align:start;text-decoration:none;text-decoration-line:none;text-decoration-style:solid;text-decoration-color:#000000;letter-spacing:normal;word-spacing:normal;text-transform:none;writing-mode:lr-tb;direction:ltr;baseline-shift:baseline;text-anchor:start;white-space:normal;clip-rule:nonzero;display:inline;overflow:visible;visibility:visible;opacity:1;isolation:auto;mix-blend-mode:normal;color-interpolation:sRGB;color-interpolation-filters:linearRGB;solid-color:#000000;solid-opacity:1;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;stroke-width:2.53707;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1;color-rendering:auto;image-rendering:auto;shape-rendering:auto;text-rendering:auto;enable-background:accumulate" />  Somatic Sarek  + style="color:#000000;font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:medium;line-height:normal;font-family:sans-serif;text-indent:0;text-align:start;text-decoration:none;text-decoration-line:none;text-decoration-style:solid;text-decoration-color:#000000;letter-spacing:normal;word-spacing:normal;text-transform:none;writing-mode:lr-tb;direction:ltr;baseline-shift:baseline;text-anchor:start;white-space:normal;clip-rule:nonzero;display:inline;overflow:visible;visibility:visible;opacity:1;isolation:auto;mix-blend-mode:normal;color-interpolation:sRGB;color-interpolation-filters:linearRGB;solid-color:#000000;solid-opacity:1;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;stroke-width:2.53707;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1;color-rendering:auto;image-rendering:auto;shape-rendering:auto;text-rendering:auto;enable-background:accumulate" /> Sarek    Exome + 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style="color:#000000;font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:medium;line-height:normal;font-family:sans-serif;text-indent:0;text-align:start;text-decoration:none;text-decoration-line:none;text-decoration-style:solid;text-decoration-color:#000000;letter-spacing:normal;word-spacing:normal;text-transform:none;writing-mode:lr-tb;direction:ltr;baseline-shift:baseline;text-anchor:start;white-space:normal;clip-rule:nonzero;display:inline;overflow:visible;visibility:visible;opacity:1;isolation:auto;mix-blend-mode:normal;color-interpolation:sRGB;color-interpolation-filters:linearRGB;solid-color:#000000;solid-opacity:1;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;stroke-width:2.53707;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1;color-rendering:auto;image-rendering:auto;shape-rendering:auto;text-rendering:auto;enable-background:accumulate" /> Sarek    Exome + style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:41.4543px;line-height:1.25;font-family:'Eurostile Extended';-inkscape-font-specification:'Eurostile Extended';text-align:start;text-anchor:start">Exome + y="117.92941" + style="stroke-width:0.264583" /> + y="27.057777" + style="stroke-width:0.264583" /> Pre-processing + style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:5.64444px;font-family:'Maven Pro';-inkscape-font-specification:'Maven Pro';stroke:#000000;stroke-width:0.264583;stroke-opacity:1">Pre-processing Genome alignment + style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:5.64444px;font-family:'Maven Pro';-inkscape-font-specification:'Maven Pro';stroke:#000000;stroke-width:0.264583;stroke-opacity:1">Genome alignment @@ -1481,86 +1482,86 @@ sodipodi:nodetypes="cc" id="path2500-5-22-5-4-7-4-07" d="m 132.06682,-28.534285 h 94.59215" - style="fill:none;stroke:#ff1465;stroke-width:2.64583325;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1" + style="fill:none;stroke:#ff1465;stroke-width:2.64583;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1" inkscape:connector-curvature="0" /> Cutadapt + style="font-style:normal;font-variant:normal;font-weight:bold;font-stretch:normal;font-size:6.35px;font-family:'DejaVu Sans Mono';-inkscape-font-specification:'DejaVu Sans Mono Bold';text-align:center;text-anchor:middle;stroke-width:0.264583" /> FastQC FastQC IGV + style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:6.35px;font-family:'Maven Pro';-inkscape-font-specification:'Maven Pro';stroke:#000000;stroke-width:0.264583;stroke-opacity:1">IGV phantompeakqualtools MultiQC @@ -1609,29 +1610,29 @@ id="flowPara5862" /> STAR BWA Peak calling & ChIP QC + style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:5.64444px;font-family:'Maven Pro';-inkscape-font-specification:'Maven Pro';stroke:#000000;stroke-width:0.264583;stroke-opacity:1">Peak calling & ChIP QC @@ -1728,10 +1729,10 @@ bigWig + style="font-style:normal;font-variant:normal;font-weight:bold;font-stretch:normal;font-size:26.231px;line-height:1.25;font-family:'Liberation Sans';-inkscape-font-specification:'Liberation Sans Bold'">bigWig + style="fill:#ffffff;stroke:#000000;stroke-width:2.64583;stroke-linecap:round;stroke-miterlimit:4;stroke-dasharray:none;paint-order:stroke markers fill" /> + style="fill:#ffffff;stroke:#000000;stroke-width:2.64583;stroke-linecap:round;stroke-miterlimit:4;stroke-dasharray:none;paint-order:stroke markers fill" /> + style="fill:#ffffff;stroke:#000000;stroke-width:2.64583;stroke-linecap:round;stroke-miterlimit:4;stroke-dasharray:none;paint-order:stroke markers fill" /> + style="fill:#ffffff;stroke:#000000;stroke-width:2.64583;stroke-linecap:round;stroke-miterlimit:4;stroke-dasharray:none;paint-order:stroke markers fill" /> Bowtie2 Chromap @@ -1840,59 +1841,59 @@ id="g1967" transform="matrix(0.2434307,0,0,0.2434307,103.90138,113.36827)"> Picard¹ + style="font-style:normal;font-variant:normal;font-weight:bold;font-stretch:normal;font-size:6.35px;font-family:'DejaVu Sans Mono';-inkscape-font-specification:'DejaVu Sans Mono Bold';text-align:center;text-anchor:middle;stroke-width:0.264583" /> Filtering² Picard + style="font-style:normal;font-variant:normal;font-weight:bold;font-stretch:normal;font-size:6.35px;font-family:'DejaVu Sans Mono';-inkscape-font-specification:'DejaVu Sans Mono Bold';text-align:center;text-anchor:middle;stroke-width:0.264583" /> Preseq + style="font-style:normal;font-variant:normal;font-weight:bold;font-stretch:normal;font-size:6.35px;font-family:'DejaVu Sans Mono';-inkscape-font-specification:'DejaVu Sans Mono Bold';text-align:center;text-anchor:middle;stroke-width:0.264583" /> Alignment QC Deeptools BedgraphtoBigWig + style="font-style:normal;font-variant:normal;font-weight:bold;font-stretch:normal;font-size:6.35px;font-family:'DejaVu Sans Mono';-inkscape-font-specification:'DejaVu Sans Mono Bold';text-align:center;text-anchor:middle;stroke-width:0.264583" /> IP enrichment analysis + style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:5.64444px;font-family:'Maven Pro';-inkscape-font-specification:'Maven Pro';stroke:#000000;stroke-width:0.264583;stroke-opacity:1">IP enrichment analysis @@ -2353,25 +2354,25 @@ sodipodi:nodetypes="cc" id="path2500-5-22-5-4-7-4-07-7-0-9-2" d="m 132.06682,-28.534285 h 94.59215" - style="fill:none;stroke:#ff1465;stroke-width:2.64583325;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1" + style="fill:none;stroke:#ff1465;stroke-width:2.64583;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1" inkscape:connector-curvature="0" /> MACS2 + id="tspan2289-4-4">MACS3 Homer Bedtools FeatureCounts R+DESeq2 XML + style="font-style:normal;font-variant:normal;font-weight:bold;font-stretch:normal;font-size:26.231px;line-height:1.25;font-family:'Liberation Sans';-inkscape-font-specification:'Liberation Sans Bold';text-align:center;direction:rtl;text-anchor:middle">XML @@ -2625,17 +2626,17 @@ + y="69.957184" + style="font-size:5.64444px;stroke:#000000;stroke-width:0.264583;stroke-opacity:1" /> 1. @@ -2669,9 +2670,9 @@ transform="matrix(0.26458333,0,0,0.26458333,-0.15701478,-103.37633)" xml:space="preserve" id="flowRoot2974-6" - style="font-style:normal;font-variant:normal;font-weight:600;font-stretch:normal;font-size:26.66666794px;line-height:1.25;font-family:'Maven Pro';-inkscape-font-specification:'Maven Pro Semi-Bold';letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none">Picard Mark duplicatesMerge alignments from multiple libraries of the same sample + style="font-style:normal;font-variant:normal;font-weight:600;font-stretch:normal;font-size:16px;line-height:0.8;font-family:'Maven Pro';-inkscape-font-specification:'Maven Pro, Semi-Bold';font-variant-ligatures:normal;font-variant-caps:normal;font-variant-numeric:diagonal-fractions;font-feature-settings:normal;text-align:start;writing-mode:lr-tb;direction:ltr;text-anchor:start" /> Pysam (paired-ends only) @@ -2735,17 +2736,17 @@ id="text76489" y="133.17679" x="482.20358" - style="font-size:4.23332977px;line-height:1.54999995;font-family:Commissioner;-inkscape-font-specification:Commissioner;letter-spacing:0px;stroke-width:0.26458299" + style="font-size:4.23333px;line-height:1.55;font-family:Commissioner;-inkscape-font-specification:Commissioner;letter-spacing:0px;stroke-width:0.264583" xml:space="preserve"> License: