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patched picard
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3 files changed

+129
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‎modules.json

+95-31
Original file line numberDiff line numberDiff line change
@@ -8,82 +8,117 @@
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"biobambam/bammarkduplicates2": {
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"branch": "main",
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"git_sha": "8909b3114d2360514c3b3514f5c5f66f7b506f8e",
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"installed_by": ["merge_dup"]
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"installed_by": [
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"merge_dup"
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]
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},
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"checkinput": {
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"branch": "main",
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"git_sha": "19d2393fd88fca055be66cbd375c0147d43d9b7f",
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"installed_by": ["stage_input"]
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"installed_by": [
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"stage_input"
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]
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},
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"payload/qcmetrics": {
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"branch": "main",
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"git_sha": "681bcc1563700f8322be1ba65305a85e169f0909",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"prep/metrics": {
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"branch": "main",
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"git_sha": "c041bcd0e203622a9ebebd720897d162a9ba95d7",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"prep/sample": {
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"branch": "main",
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"git_sha": "19d2393fd88fca055be66cbd375c0147d43d9b7f",
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"installed_by": ["stage_input"]
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"installed_by": [
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"stage_input"
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]
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},
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"samtools/convert": {
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"branch": "main",
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"git_sha": "8909b3114d2360514c3b3514f5c5f66f7b506f8e",
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"installed_by": ["merge_dup", "modules"]
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"installed_by": [
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"merge_dup",
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"modules"
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]
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},
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"samtools/index": {
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"branch": "main",
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"git_sha": "e1f2b946b457eac191c0fa97ae1d159a15874c6b",
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"installed_by": ["merge_dup", "stage_input"]
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"installed_by": [
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"merge_dup",
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"stage_input"
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]
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},
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"samtools/merge": {
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"branch": "main",
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"git_sha": "8909b3114d2360514c3b3514f5c5f66f7b506f8e",
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"installed_by": ["merge_dup", "modules"]
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"installed_by": [
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"merge_dup",
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"modules"
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]
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},
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"score/download": {
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"branch": "main",
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"git_sha": "19ee48fdf1672ef9723e3093531be7ddea3e27ec",
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"installed_by": ["song_score_download"]
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"installed_by": [
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"song_score_download"
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]
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},
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"score/upload": {
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"branch": "main",
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"git_sha": "19ee48fdf1672ef9723e3093531be7ddea3e27ec",
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"installed_by": ["song_score_upload"]
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"installed_by": [
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"song_score_upload"
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]
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},
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"song/get": {
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"branch": "main",
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"git_sha": "19ee48fdf1672ef9723e3093531be7ddea3e27ec",
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"installed_by": ["song_score_download"]
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"installed_by": [
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"song_score_download"
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]
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},
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"song/manifest": {
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"branch": "main",
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"git_sha": "19ee48fdf1672ef9723e3093531be7ddea3e27ec",
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"installed_by": ["song_score_upload"]
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"installed_by": [
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"song_score_upload"
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]
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},
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"song/publish": {
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"branch": "main",
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"git_sha": "19ee48fdf1672ef9723e3093531be7ddea3e27ec",
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"installed_by": ["song_score_upload"]
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"installed_by": [
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"song_score_upload"
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]
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},
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"song/submit": {
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"branch": "main",
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"git_sha": "19ee48fdf1672ef9723e3093531be7ddea3e27ec",
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"installed_by": ["song_score_upload"]
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"installed_by": [
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"song_score_upload"
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]
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},
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"tabix/tabix": {
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"branch": "main",
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"git_sha": "e1f2b946b457eac191c0fa97ae1d159a15874c6b",
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"installed_by": ["stage_input"]
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"installed_by": [
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"stage_input"
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]
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},
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"tar": {
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"branch": "main",
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"git_sha": "8909b3114d2360514c3b3514f5c5f66f7b506f8e",
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"installed_by": ["merge_dup"]
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"installed_by": [
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"merge_dup"
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]
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}
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}
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},
@@ -92,22 +127,30 @@
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"merge_dup": {
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"branch": "main",
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"git_sha": "faa9ed09e9fc7eff2a441fbb31c4991df3fa87b5",
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"installed_by": ["subworkflows"]
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"installed_by": [
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"subworkflows"
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]
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},
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"song_score_download": {
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"branch": "main",
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"git_sha": "92aa620385099e94401c22b8633cc55ed34ca10e",
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"installed_by": ["stage_input"]
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"installed_by": [
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"stage_input"
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]
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},
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"song_score_upload": {
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"branch": "main",
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"git_sha": "92aa620385099e94401c22b8633cc55ed34ca10e",
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"installed_by": ["subworkflows"]
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"installed_by": [
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"subworkflows"
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]
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},
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"stage_input": {
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"branch": "main",
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"git_sha": "19d2393fd88fca055be66cbd375c0147d43d9b7f",
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"installed_by": ["subworkflows"]
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"installed_by": [
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"subworkflows"
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]
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}
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}
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}
@@ -118,55 +161,76 @@
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"fastqc": {
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"branch": "master",
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"git_sha": "f4ae1d942bd50c5c0b9bd2de1393ce38315ba57c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"hisat2/align": {
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"branch": "master",
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"git_sha": "4eed099a12a7d586ce830a662a33a9df5bd67a24",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"multiqc": {
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"branch": "master",
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"git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"picard/collectrnaseqmetrics": {
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"branch": "master",
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"git_sha": "20b0918591d4ba20047d7e13e5094bcceba81447",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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],
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"patch": "modules/nf-core/picard/collectrnaseqmetrics/picard-collectrnaseqmetrics.diff"
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},
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"samtools/flagstat": {
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"branch": "master",
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"git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"samtools/idxstats": {
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"branch": "master",
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"git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"samtools/index": {
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"branch": "master",
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"git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"samtools/sort": {
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"branch": "master",
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"git_sha": "4352dbdb09ec40db71e9b172b97a01dcf5622c26",
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"installed_by": ["bam_sort_stats_samtools"]
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"installed_by": [
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"bam_sort_stats_samtools"
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]
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},
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"samtools/stats": {
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"branch": "master",
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"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"star/align": {
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"branch": "master",
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"git_sha": "cd22a76c78b09f7837a5a75642774a4bf48c92ba",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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}
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}
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}
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}
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}
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}
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}

‎modules/nf-core/picard/collectrnaseqmetrics/main.nf

+1-1
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‎modules/nf-core/picard/collectrnaseqmetrics/picard-collectrnaseqmetrics.diff

+33
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