cramstats

tests/.nftignore

@@ -25,7 +25,7 @@ reports/EnsemblVEP/*/*.ann.summary.html
 reports/fastp/**/*.fastp.{log,html}
 reports/fastqc/**/*_fastqc.{html,zip}
 reports/markduplicates/**/*.md.cram.metrics
-reports/samtools/**/**.recal.cram.stats
+reports/samtools/**/**.cram.stats
 reports/snpeff/*/*_snpEff.csv
 reports/snpeff/*/snpEff_summary.html
 reports/vcftools/**/*.TsTv.qual

tests/alignment_from_everything.nf.test.snap

@@ -398,15 +398,7 @@
                 "test_bam.recal.mosdepth.region.dist.txt:md5,75e1ce7e55af51f4985fa91654a5ea2d",
                 "test_bam.recal.mosdepth.summary.txt:md5,dbe376360e437c89190139ef0ae6769a",
                 "test_bam.recal.regions.bed.gz:md5,0e5ed846b9b11717e42e93eec60f4ffc",
-                "test_bam.recal.regions.bed.gz.csi:md5,633cc0252eb2246a0943aec7e7512e3e",
-                "test.md.cram.stats:md5,7d0a7d3d4ca6bf21702e7775b1777fb8",
-                "test.recal.cram.stats:md5,269fd4151ac69c1de63e2224310386a0",
-                "test2.md.cram.stats:md5,9036c85b25e11a3340a6c1006a8d614a",
-                "test2.recal.cram.stats:md5,816dbaf70f47a5f44444a97282a6bbb0",
-                "test3.md.cram.stats:md5,d8cfbfe40816feedcbc30aba0ae863a5",
-                "test3.recal.cram.stats:md5,46a3b9cf59fd06bf6c4b8f91b18d4f01",
-                "test_bam.md.cram.stats:md5,742cc3262b1c1b0710092b5288ed9d9a",
-                "test_bam.recal.cram.stats:md5,0459edb604f03ef29359826eb60a44a9"
+                "test_bam.recal.regions.bed.gz.csi:md5,633cc0252eb2246a0943aec7e7512e3e"
             ],
             "No CRAM files",
             [
@@ -466,4 +458,4 @@
         },
         "timestamp": "2025-03-10T11:13:03.085460403"
     }
-}
+}

tests/alignment_to_fastq.nf.test.snap

@@ -267,9 +267,7 @@
                 "test.recal.mosdepth.region.dist.txt:md5,75e1ce7e55af51f4985fa91654a5ea2d",
                 "test.recal.mosdepth.summary.txt:md5,dbe376360e437c89190139ef0ae6769a",
                 "test.recal.regions.bed.gz:md5,0e5ed846b9b11717e42e93eec60f4ffc",
-                "test.recal.regions.bed.gz.csi:md5,633cc0252eb2246a0943aec7e7512e3e",
-                "test.md.cram.stats:md5,2cc3430db9e2007da1464dd616aa8427",
-                "test.recal.cram.stats:md5,1ef19ce72bf2cb61d2dc4aede12bec94"
+                "test.recal.regions.bed.gz.csi:md5,633cc0252eb2246a0943aec7e7512e3e"
             ],
             "No CRAM files",
             [

tests/concatenation.nf.test.snap

@@ -208,8 +208,6 @@
                 "testT.recal.mosdepth.summary.txt:md5,024649a659caff330dfbef4ac3560542",
                 "testT.recal.regions.bed.gz:md5,14b36a2cf428840aab471f95cfbe399f",
                 "testT.recal.regions.bed.gz.csi:md5,c5d0be930ffc9e562f21519a0d488d5d",
-                "testN.recal.cram.stats:md5,a15b3a5e59337db312d66020c7bb93ac",
-                "testT.recal.cram.stats:md5,fae549c0c944f6cc34dd6d9b9569e3d3",
                 "testN.freebayes.FILTER.summary:md5,2ec507a210cf7de0425b6c8028a6edf8",
                 "testN.freebayes.TsTv.count:md5,4913577b275634ea33077dd023325dee",
                 "testT.freebayes.FILTER.summary:md5,50f90bd0cdd1e95c10d7e5d88d0346f8",

tests/default.nf.test.snap

@@ -299,8 +299,6 @@
                 "test.recal.mosdepth.summary.txt:md5,839108358878ada89e1eaddf6e0541ba",
                 "test.recal.regions.bed.gz:md5,6fdaec99e739dc0f47fe55dd64dfe93e",
                 "test.recal.regions.bed.gz.csi:md5,5f9c60279af78e3aeafc96a8c11fb35f",
-                "test.md.cram.stats:md5,7d19da3fc342afe0884c944f97a578b1",
-                "test.recal.cram.stats:md5,820d123e746d1abdc90fd8710828082e",
                 "test.strelka.variants.FILTER.summary:md5,ad417bc96d31223f61170987975d8128",
                 "test.strelka.variants.TsTv.count:md5,fa27f678965b7cba6a92efcd039f802a"
             ],

tests/fastp.nf.test.snap

@@ -330,8 +330,7 @@
                 "test.recal.mosdepth.region.dist.txt:md5,3e33ce923c2e9348c001cc34960d4d90",
                 "test.recal.mosdepth.summary.txt:md5,2de9c6803d74a7157c626320cf916587",
                 "test.recal.regions.bed.gz:md5,bb0ca9679342566559b7c5ed0b4e25b3",
-                "test.recal.regions.bed.gz.csi:md5,eba5aca0b8f72759192bbdd29330278e",
-                "test.md.cram.stats:md5,f44dadb50affac49500eefad04cb77ea"
+                "test.recal.regions.bed.gz.csi:md5,eba5aca0b8f72759192bbdd29330278e"
             ],
             "No BAM files",
             [
@@ -706,8 +705,7 @@
                 "test.recal.mosdepth.region.dist.txt:md5,1266123c1dd631e97aaf82a63162ed33",
                 "test.recal.mosdepth.summary.txt:md5,8d6d2a2d898fbf2e5bb4954c3a5857d9",
                 "test.recal.regions.bed.gz:md5,e8d15607e26a3d7c4f045fde542e129b",
-                "test.recal.regions.bed.gz.csi:md5,a3ac5a5d620082a4a1061656742d8e30",
-                "test.md.cram.stats:md5,f0c2d695d79101af0e4beb53239f5a9e"
+                "test.recal.regions.bed.gz.csi:md5,a3ac5a5d620082a4a1061656742d8e30"
             ],
             "No BAM files",
             [

tests/sentieon.nf.test.snap

@@ -217,8 +217,6 @@
                 "test.recal.summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "test.recal.thresholds.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
                 "test.recal.thresholds.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "test.md.cram.stats:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "test.recal.cram.stats:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "test.strelka.variants.012:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "test.strelka.variants.012.indv:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "test.strelka.variants.012.pos:md5,d41d8cd98f00b204e9800998ecf8427e",

tests/start_from_markduplicates.nf.test.snap

@@ -111,8 +111,7 @@
                 "test.sorted.mosdepth.region.dist.txt:md5,f1f1ad86fc280bced1888a5d7d25a3f2",
                 "test.sorted.mosdepth.summary.txt:md5,32ea70ef1b99def3dc900b4afd513a40",
                 "test.sorted.regions.bed.gz:md5,07bbc084a889f1cece4307fd00214a6e",
-                "test.sorted.regions.bed.gz.csi:md5,c5d0be930ffc9e562f21519a0d488d5d",
-                "test.sorted.cram.stats:md5,a15b3a5e59337db312d66020c7bb93ac"
+                "test.sorted.regions.bed.gz.csi:md5,c5d0be930ffc9e562f21519a0d488d5d"
             ],
             "No CRAM files",
             "No BAM files"
@@ -281,9 +280,7 @@
                 "test.recal.mosdepth.region.dist.txt:md5,75e1ce7e55af51f4985fa91654a5ea2d",
                 "test.recal.mosdepth.summary.txt:md5,b23cf96942b2ada3f41172a9349a1175",
                 "test.recal.regions.bed.gz:md5,74cd0c779c7b3228adcf3b177333886a",
-                "test.recal.regions.bed.gz.csi:md5,080731cdedcd389e72135f048d6e2e00",
-                "test.md.cram.stats:md5,f181d98f08ad94c3926ac149a87d834b",
-                "test.recal.cram.stats:md5,18346c938c7b1bfaf9ac9413fdba90d8"
+                "test.recal.regions.bed.gz.csi:md5,080731cdedcd389e72135f048d6e2e00"
             ],
             [
                 [
@@ -434,9 +431,7 @@
                 "test.sorted.mosdepth.region.dist.txt:md5,f1f1ad86fc280bced1888a5d7d25a3f2",
                 "test.sorted.mosdepth.summary.txt:md5,32ea70ef1b99def3dc900b4afd513a40",
                 "test.sorted.regions.bed.gz:md5,07bbc084a889f1cece4307fd00214a6e",
-                "test.sorted.regions.bed.gz.csi:md5,c5d0be930ffc9e562f21519a0d488d5d",
-                "test.recal.cram.stats:md5,9f75ec16d22ce12c348cbd7477c9886e",
-                "test.sorted.cram.stats:md5,308a4213cc2ea25cbdd6d58b562673a5"
+                "test.sorted.regions.bed.gz.csi:md5,c5d0be930ffc9e562f21519a0d488d5d"
             ],
             [
                 [
@@ -610,9 +605,7 @@
                 "test.recal.mosdepth.region.dist.txt:md5,75e1ce7e55af51f4985fa91654a5ea2d",
                 "test.recal.mosdepth.summary.txt:md5,b23cf96942b2ada3f41172a9349a1175",
                 "test.recal.regions.bed.gz:md5,74cd0c779c7b3228adcf3b177333886a",
-                "test.recal.regions.bed.gz.csi:md5,080731cdedcd389e72135f048d6e2e00",
-                "test.md.cram.stats:md5,f181d98f08ad94c3926ac149a87d834b",
-                "test.recal.cram.stats:md5,18346c938c7b1bfaf9ac9413fdba90d8"
+                "test.recal.regions.bed.gz.csi:md5,080731cdedcd389e72135f048d6e2e00"
             ],
             [
                 [

tests/start_from_preparerecalibration.nf.test.snap

@@ -394,8 +394,7 @@
                 "test.recal.mosdepth.region.dist.txt:md5,f1f1ad86fc280bced1888a5d7d25a3f2",
                 "test.recal.mosdepth.summary.txt:md5,32ea70ef1b99def3dc900b4afd513a40",
                 "test.recal.regions.bed.gz:md5,07bbc084a889f1cece4307fd00214a6e",
-                "test.recal.regions.bed.gz.csi:md5,c5d0be930ffc9e562f21519a0d488d5d",
-                "test.recal.cram.stats:md5,9f75ec16d22ce12c348cbd7477c9886e"
+                "test.recal.regions.bed.gz.csi:md5,c5d0be930ffc9e562f21519a0d488d5d"
             ],
             "No BAM files",
             [

tests/start_from_recalibration.nf.test.snap

@@ -50,8 +50,7 @@
                 "test.recal.mosdepth.region.dist.txt:md5,f1f1ad86fc280bced1888a5d7d25a3f2",
                 "test.recal.mosdepth.summary.txt:md5,32ea70ef1b99def3dc900b4afd513a40",
                 "test.recal.regions.bed.gz:md5,07bbc084a889f1cece4307fd00214a6e",
-                "test.recal.regions.bed.gz.csi:md5,c5d0be930ffc9e562f21519a0d488d5d",
-                "test.recal.cram.stats:md5,1aacf5ac46a0e600925934cf9ee92fc4"
+                "test.recal.regions.bed.gz.csi:md5,c5d0be930ffc9e562f21519a0d488d5d"
             ],
             "No BAM files",
             [
@@ -352,7 +351,7 @@
             ],
             "No BAM files",
             [
-                
+
             ]
         ],
         "meta": {

tests/tumor-normal-pair.nf.test.snap

@@ -353,10 +353,6 @@
                 "test2.recal.mosdepth.summary.txt:md5,8b991358768cade225470a07cd34f573",
                 "test2.recal.regions.bed.gz:md5,08e767f91a0a8d82733f0040e804a85f",
                 "test2.recal.regions.bed.gz.csi:md5,eba5aca0b8f72759192bbdd29330278e",
-                "test.md.cram.stats:md5,7d0a7d3d4ca6bf21702e7775b1777fb8",
-                "test.recal.cram.stats:md5,269fd4151ac69c1de63e2224310386a0",
-                "test2.md.cram.stats:md5,592aae2575ef68c8c8d9e993ca288f2d",
-                "test2.recal.cram.stats:md5,47c5ad8a7d4221d03673fd67388f9960",
                 "test.strelka.variants.FILTER.summary:md5,dd87f507da7de20d5318841af312493b",
                 "test.strelka.variants.TsTv.count:md5,fa27f678965b7cba6a92efcd039f802a",
                 "test2_vs_test.strelka.somatic_indels.FILTER.summary:md5,1ce42d34e4ae919afb519efc99146423",

tests/variant_calling_cnvkit.nf.test.snap

@@ -139,10 +139,6 @@
                 "sample4.recal.mosdepth.summary.txt:md5,7141030385af1f653718c9e0c9a5be80",
                 "sample4.recal.regions.bed.gz:md5,c680c5d75f0cea068e3f917f4cf9bf52",
                 "sample4.recal.regions.bed.gz.csi:md5,4003c8833ed5e9b9f45282a6915c935e",
-                "sample1.recal.cram.stats:md5,bcc229318527e414e69aaa5cd092ad9b",
-                "sample2.recal.cram.stats:md5,0d1784cb4c3f14b9858247ac6128dd03",
-                "sample3.recal.cram.stats:md5,bcc229318527e414e69aaa5cd092ad9b",
-                "sample4.recal.cram.stats:md5,0d1784cb4c3f14b9858247ac6128dd03",
                 "multi_intervals.antitarget.bed:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "multi_intervals.target.bed:md5,f7474a0afbf5565c5675916606f2d9bd",
                 "reference.cnn:md5,891454915f82d0eeda0be13d71e0d5d7",
@@ -272,7 +268,6 @@
                 "sample1.recal.mosdepth.summary.txt:md5,d7676e7c1de851b0ee5185d21096123b",
                 "sample1.recal.regions.bed.gz:md5,6edeb8f7041a4403cb73651744b5bc82",
                 "sample1.recal.regions.bed.gz.csi:md5,f17cc9d960aa4a1e96548d570585cc8a",
-                "sample1.recal.cram.stats:md5,bcc229318527e414e69aaa5cd092ad9b",
                 "multi_intervals.antitarget.bed:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "multi_intervals.target.bed:md5,f7474a0afbf5565c5675916606f2d9bd",
                 "reference.cnn:md5,891454915f82d0eeda0be13d71e0d5d7",
@@ -399,8 +394,6 @@
                 "sample4.recal.mosdepth.summary.txt:md5,7141030385af1f653718c9e0c9a5be80",
                 "sample4.recal.regions.bed.gz:md5,c680c5d75f0cea068e3f917f4cf9bf52",
                 "sample4.recal.regions.bed.gz.csi:md5,4003c8833ed5e9b9f45282a6915c935e",
-                "sample3.recal.cram.stats:md5,bcc229318527e414e69aaa5cd092ad9b",
-                "sample4.recal.cram.stats:md5,0d1784cb4c3f14b9858247ac6128dd03",
                 "multi_intervals.antitarget.bed:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "multi_intervals.target.bed:md5,f7474a0afbf5565c5675916606f2d9bd",
                 "reference.cnn:md5,891454915f82d0eeda0be13d71e0d5d7",
@@ -514,7 +507,6 @@
                 "sample2.recal.mosdepth.summary.txt:md5,7141030385af1f653718c9e0c9a5be80",
                 "sample2.recal.regions.bed.gz:md5,c680c5d75f0cea068e3f917f4cf9bf52",
                 "sample2.recal.regions.bed.gz.csi:md5,4003c8833ed5e9b9f45282a6915c935e",
-                "sample2.recal.cram.stats:md5,0d1784cb4c3f14b9858247ac6128dd03",
                 "cnvkit.reference.antitarget-tmp.bed:md5,3d4d20f9f23b39970865d29ef239d20b",
                 "cnvkit.reference.target-tmp.bed:md5,657b25dbda8516624efa8cb2cf3716ca",
                 "test2.paired_end.recalibrated.sorted-scatter.png:md5,d9a4a27a7a93eca23108b43dea09c140",

tests/variant_calling_controlfreec.nf.test.snap

@@ -113,8 +113,6 @@
                 "sample4.recal.summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "sample4.recal.thresholds.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
                 "sample4.recal.thresholds.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "sample3.recal.cram.stats:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "sample4.recal.cram.stats:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "GC_profile.sample4_vs_sample3.cpn:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "sample4_vs_sample3.bed:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "sample4_vs_sample3.circos.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
@@ -232,8 +230,6 @@
                 "sample4.recal.per-base.bed.gz.csi:md5,aaa7bed9e7ef873b23bca249b8b58eb9",
                 "sample4.recal.regions.bed.gz:md5,b7561bc56a955f7db0f11e67e2ec0386",
                 "sample4.recal.regions.bed.gz.csi:md5,538cb5d244411a670a4b041691f8825b",
-                "sample3.recal.cram.stats:md5,bcc229318527e414e69aaa5cd092ad9b",
-                "sample4.recal.cram.stats:md5,0d1784cb4c3f14b9858247ac6128dd03",
                 "sample4_vs_sample3.bed:md5,47f60179409e9389e59b2e2525e42210",
                 "sample4_vs_sample3.circos.txt:md5,68addb1d8bda08355842bef0ab15cd6e",
                 "sample4_vs_sample3.normal.mpileup.gz_control.cpn:md5,d50bf2c9a4d35f022364901c284e80ed",
@@ -339,7 +335,6 @@
                 "sample2.recal.summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "sample2.recal.thresholds.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
                 "sample2.recal.thresholds.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "sample2.recal.cram.stats:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "GC_profile.sample2.cpn:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "sample2.bed:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "sample2.circos.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
@@ -436,7 +431,6 @@
                 "sample2.recal.mosdepth.summary.txt:md5,0a7300e56eda6fba7c7564f00aa000f0",
                 "sample2.recal.per-base.bed.gz:md5,39a1bc436aa8546c26faedbe94cb676c",
                 "sample2.recal.per-base.bed.gz.csi:md5,aaa7bed9e7ef873b23bca249b8b58eb9",
-                "sample2.recal.cram.stats:md5,0d1784cb4c3f14b9858247ac6128dd03",
                 "sample2.bed:md5,5249f46e614b60867bdd6b9b83327979",
                 "sample2.circos.txt:md5,2efab24d023931cec8b158c56d1f1765",
                 "sample2.p.value.txt:md5,38c8c9ad33a4fca3804a34d5c436cd1e",

tests/variant_calling_freebayes.nf.test.snap

@@ -133,7 +133,6 @@
                 "sample2.recal.per-base.bed.gz.csi:md5,aaa7bed9e7ef873b23bca249b8b58eb9",
                 "sample2.recal.regions.bed.gz:md5,b7561bc56a955f7db0f11e67e2ec0386",
                 "sample2.recal.regions.bed.gz.csi:md5,538cb5d244411a670a4b041691f8825b",
-                "sample2.recal.cram.stats:md5,0d1784cb4c3f14b9858247ac6128dd03",
                 "sample2.freebayes.FILTER.summary:md5,0df3ddeec5779344b5d463347c9c6ea8",
                 "sample2.freebayes.TsTv.count:md5,b1d308ed5087361a584cb61e7b835e1e"
             ]
@@ -475,8 +474,6 @@
                 "test.recal.per-base.bed.gz.csi:md5,bb424ead65ffe782f6eaa3663ea65721",
                 "test.recal.regions.bed.gz:md5,e39c27885a30c0321f3cb7c7fb6c5edc",
                 "test.recal.regions.bed.gz.csi:md5,e1a52ced0e9ded1eecbca4eff2014c8e",
-                "test.md.cram.stats:md5,7d19da3fc342afe0884c944f97a578b1",
-                "test.recal.cram.stats:md5,87ed0ca7a04c0b6dfc5f05b18467ecbe",
                 "test.freebayes.FILTER.summary:md5,75824ce08910acce7e9f6adb4d635850",
                 "test.freebayes.TsTv.count:md5,3c198f7ec7fe2f5d365218ba0ff64197"
             ],
@@ -876,10 +873,6 @@
                 "test2.recal.per-base.bed.gz.csi:md5,49dec4905343693cb7812da9ee60037c",
                 "test2.recal.regions.bed.gz:md5,0bb2549180165a99680ba3e453ea312f",
                 "test2.recal.regions.bed.gz.csi:md5,e1a52ced0e9ded1eecbca4eff2014c8e",
-                "test.md.cram.stats:md5,7d0a7d3d4ca6bf21702e7775b1777fb8",
-                "test.recal.cram.stats:md5,4efd4142116c0ddc309aa3660834d991",
-                "test2.md.cram.stats:md5,592aae2575ef68c8c8d9e993ca288f2d",
-                "test2.recal.cram.stats:md5,9ac6a5c9280fa139e8597a41aadabbb5",
                 "test.freebayes.FILTER.summary:md5,43d53e36cbb1091f915b2499e545b41e",
                 "test.freebayes.TsTv.count:md5,650f3dc78c5aaaecfe8ffa3d499e812f",
                 "test2_vs_test.freebayes.FILTER.summary:md5,84039d55edf0981d6b9b81252aff6741",
@@ -1258,10 +1251,6 @@
                 "test2.recal.mosdepth.summary.txt:md5,d5e4084de2ea2a0a7b60b2d71c804d4b",
                 "test2.recal.per-base.bed.gz:md5,e1c6d60621d8f64aaf28fa1c1ddda921",
                 "test2.recal.per-base.bed.gz.csi:md5,69f4da029c05e9bcccae8895b6247a1e",
-                "test.md.cram.stats:md5,7d0a7d3d4ca6bf21702e7775b1777fb8",
-                "test.recal.cram.stats:md5,478a0a01a1d1e2f2a5c0d91c58d32d84",
-                "test2.md.cram.stats:md5,592aae2575ef68c8c8d9e993ca288f2d",
-                "test2.recal.cram.stats:md5,bada0a59a5497724fc71620d999e1460",
                 "test.freebayes.FILTER.summary:md5,76c5919541536c12b5c8a6094d6d78d5",
                 "test.freebayes.TsTv.count:md5,0a0464beef110bc0f3c5a35d022b528e",
                 "test2_vs_test.freebayes.FILTER.summary:md5,d2d717fef7c18ef9b40bbbc5c5bbf101",
@@ -1604,8 +1593,6 @@
                 "test.recal.mosdepth.summary.txt:md5,839108358878ada89e1eaddf6e0541ba",
                 "test.recal.regions.bed.gz:md5,6fdaec99e739dc0f47fe55dd64dfe93e",
                 "test.recal.regions.bed.gz.csi:md5,5f9c60279af78e3aeafc96a8c11fb35f",
-                "test.md.cram.stats:md5,7d19da3fc342afe0884c944f97a578b1",
-                "test.recal.cram.stats:md5,4242101f58b473ca012a8162e45ff7d4",
                 "test.freebayes.FILTER.summary:md5,562eaa4512cd4b57e6cfca7b44957d1c",
                 "test.freebayes.TsTv.count:md5,4e6935b1e1906e57be1b54c0dffe7169"
             ],
@@ -1753,7 +1740,6 @@
                 "sample2.recal.mosdepth.summary.txt:md5,0a7300e56eda6fba7c7564f00aa000f0",
                 "sample2.recal.per-base.bed.gz:md5,39a1bc436aa8546c26faedbe94cb676c",
                 "sample2.recal.per-base.bed.gz.csi:md5,aaa7bed9e7ef873b23bca249b8b58eb9",
-                "sample2.recal.cram.stats:md5,0d1784cb4c3f14b9858247ac6128dd03",
                 "sample2.freebayes.FILTER.summary:md5,ee513ecf779b6e201b8ef98f95f25aab",
                 "sample2.freebayes.TsTv.count:md5,2dc153ad5af26c9f8aa82442bf65b4bf"
             ]