diff --git a/conf/modules.config b/conf/modules.config
index 8b27c3a2..4e763048 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -439,6 +439,12 @@ process {
         ]
     }
 
+    withName: BED2SAF  {
+        publishDir = [
+            enabled: false
+        ]
+    }
+
     withName: SUBREAD_FEATURECOUNTS_PREDICTED {
         ext.prefix = { "${meta.id}-group_${annotation.baseName}-transcripts" }
         ext.args = '-F "SAF"'
diff --git a/tests/.nftignore b/tests/.nftignore
index a3c36709..ba48e962 100644
--- a/tests/.nftignore
+++ b/tests/.nftignore
@@ -26,6 +26,7 @@ pipeline_info/*.{html,json,txt,yml}
 **/*.pdf
 
 transcript_identification/homer/*_tagdir/*
+transcript_identification/filtered/*_filtered.bed
 transcript_identification/intersect/*_intersect.bed
 
 quality_control/bbsplit/*.stats.txt
diff --git a/workflows/tests/aligner/bowtie2.nf.test.snap b/workflows/tests/aligner/bowtie2.nf.test.snap
index 24d33f9b..65f2d4a2 100644
--- a/workflows/tests/aligner/bowtie2.nf.test.snap
+++ b/workflows/tests/aligner/bowtie2.nf.test.snap
@@ -311,8 +311,6 @@
                 "cd4_REP1.trimmed.fastp.json:md5,bd9a3344c1591d6be4d524451f9dca53",
                 "cd4_REP2.trimmed.fastp.json:md5,bc6e3f9ff7835f220535cc393b8eb25f",
                 "jurkat.trimmed.fastp.json:md5,65f7247a87479c7157c7357d575336e2",
-                "cd4_filtered.bed:md5,c8bb282144d8078c0e4c809fe0878a12",
-                "jurkat_filtered.bed:md5,1341da464eab0ef94e921de514f46495",
                 "cd4.bed:md5,c311e32ebdca7f3e978a271407de7241",
                 "cd4.peaks.txt:md5,66589ceaf2aabf1e4e7bad64b94b6fd8",
                 "jurkat.bed:md5,5e170e72c4e2b27a7bb0a6de7b735c1c",
diff --git a/workflows/tests/aligner/bwa.nf.test.snap b/workflows/tests/aligner/bwa.nf.test.snap
index 73873d96..cd341d37 100644
--- a/workflows/tests/aligner/bwa.nf.test.snap
+++ b/workflows/tests/aligner/bwa.nf.test.snap
@@ -111,8 +111,6 @@
                 }
             },
             [
-                "bed2saf",
-                "bed2saf/cd4_intersect.saf",
                 "bwa",
                 "bwa/cd4_REP1.sorted.bam",
                 "bwa/cd4_REP1.sorted.bam.bai",
@@ -391,7 +389,6 @@
                 "transcript_identification/pints/jurkat_chr21_1_unidirectional_peaks.bed"
             ],
             [
-                "cd4_intersect.saf:md5,635fcd8e2c060dc75db25564c2a664dc",
                 "cd4_REP1.sorted.bam.flagstat:md5,863e2d506d5cc4239af98a5f31bbc906",
                 "cd4_REP1.sorted.bam.idxstats:md5,b1dd8bcbd23c53c21f0e11082d9315f2",
                 "cd4_REP1.sorted.bam.stats:md5,1536c80bae78b2062508e1de210f6387",
@@ -448,8 +445,6 @@
                 "cd4_REP4.trimmed.fastp.json:md5,c073bd26609ddca91396d0f374ec5b80",
                 "jurkat_REP1.trimmed.fastp.json:md5,329fd8e56421a196fc2ebd37ab3bc22d",
                 "jurkat_REP2.trimmed.fastp.json:md5,8bad5b02a27e5386255b998a6a69db15",
-                "cd4_filtered.bed:md5,9765d778862a20feefb94d407773bef3",
-                "jurkat_filtered.bed:md5,cae11a1bfb707ea2df5fe612ae7268c8",
                 "cd4.bed:md5,ab94918610a560772fdbec591200295f",
                 "cd4.peaks.txt:md5,6edefe0a75b76240d3b49d12e49cb600",
                 "jurkat.bed:md5,41908723fa423a78476feb2e7627a3a4",
diff --git a/workflows/tests/aligner/bwamem2.nf.test.snap b/workflows/tests/aligner/bwamem2.nf.test.snap
index d9f62564..be3f1f96 100644
--- a/workflows/tests/aligner/bwamem2.nf.test.snap
+++ b/workflows/tests/aligner/bwamem2.nf.test.snap
@@ -106,8 +106,6 @@
                 }
             },
             [
-                "bed2saf",
-                "bed2saf/cd4_intersect.saf",
                 "bwamem2",
                 "bwamem2/cd4_REP1.sorted.bam",
                 "bwamem2/cd4_REP1.sorted.bam.bai",
@@ -308,7 +306,6 @@
                 "transcript_identification/pints/jurkat_chr21_1_unidirectional_peaks.bed"
             ],
             [
-                "cd4_intersect.saf:md5,2528ed58898f6e1f9d3d54fc1381c4c6",
                 "cd4_REP1.sorted.bam.flagstat:md5,863e2d506d5cc4239af98a5f31bbc906",
                 "cd4_REP1.sorted.bam.idxstats:md5,b1dd8bcbd23c53c21f0e11082d9315f2",
                 "cd4_REP1.sorted.bam.stats:md5,1536c80bae78b2062508e1de210f6387",
@@ -338,8 +335,6 @@
                 "cd4_REP1.trimmed.fastp.json:md5,bd9a3344c1591d6be4d524451f9dca53",
                 "cd4_REP2.trimmed.fastp.json:md5,bc6e3f9ff7835f220535cc393b8eb25f",
                 "jurkat.trimmed.fastp.json:md5,65f7247a87479c7157c7357d575336e2",
-                "cd4_filtered.bed:md5,fe48a92889bc118c41e436989f85c65e",
-                "jurkat_filtered.bed:md5,f1dde43c4ad9dec972ff9fa38cc6f2fe",
                 "cd4.bed:md5,b55e5290d78941f36c3d1ecfef8e0062",
                 "cd4.peaks.txt:md5,bdcd2ec3a56a8a4a01ed19e17da003f2",
                 "jurkat.bed:md5,383cfaf10535dbe5d7f47607e345f4cb",
diff --git a/workflows/tests/aligner/hisat2.nf.test.snap b/workflows/tests/aligner/hisat2.nf.test.snap
index 7e28c8f6..c7ba4cd7 100644
--- a/workflows/tests/aligner/hisat2.nf.test.snap
+++ b/workflows/tests/aligner/hisat2.nf.test.snap
@@ -332,8 +332,6 @@
                 "cd4_REP1.trimmed.fastp.json:md5,bd9a3344c1591d6be4d524451f9dca53",
                 "cd4_REP2.trimmed.fastp.json:md5,bc6e3f9ff7835f220535cc393b8eb25f",
                 "jurkat.trimmed.fastp.json:md5,65f7247a87479c7157c7357d575336e2",
-                "cd4_filtered.bed:md5,057f04ad44d3c2bf223be225b390fe0e",
-                "jurkat_filtered.bed:md5,bd6458d033db136523d32ffba259f564",
                 "cd4.bed:md5,d8c78818eb1666575ef4c2534ea3727e",
                 "cd4.peaks.txt:md5,8bb1c5655a1cce187290a3409e82a43b",
                 "jurkat.bed:md5,7298daa579135dfb8924067abaa2ba4e",
diff --git a/workflows/tests/aligner/star.nf.test.snap b/workflows/tests/aligner/star.nf.test.snap
index c441f1d3..92891148 100644
--- a/workflows/tests/aligner/star.nf.test.snap
+++ b/workflows/tests/aligner/star.nf.test.snap
@@ -94,8 +94,6 @@
                 }
             },
             [
-                "bed2saf",
-                "bed2saf/cd4_intersect.saf",
                 "cat",
                 "cat/cd4.bed",
                 "cat/jurkat.bed",
@@ -330,7 +328,6 @@
                 "transcript_identification/pints/jurkat_chr21_1_unidirectional_peaks.bed"
             ],
             [
-                "cd4_intersect.saf:md5,2528ed58898f6e1f9d3d54fc1381c4c6",
                 "cd4.bed:md5,26765aa153cb1d6bb668f5786da5763e",
                 "jurkat.bed:md5,15a3bec7a3ffb53c1e621665b3f45873",
                 "cd4_REP1.dreg.bedGraph:md5,6ecfb93ba1a56308ce7d3c4703e0e5e3",
@@ -391,8 +388,6 @@
                 "sjdbList.fromGTF.out.tab:md5,5d9761b49920fb70a77d74e390d196b9",
                 "sjdbList.out.tab:md5,766fbca932681f8666b3a9e5fb3640bd",
                 "transcriptInfo.tab:md5,21c1f470ffe3b55b23900e7b7eaec2f4",
-                "cd4_filtered.bed:md5,57cde1c26fabdc9c416326ba825b3f15",
-                "jurkat_filtered.bed:md5,95a5279ec2387dfa0b4c2e7820083527",
                 "cd4.bed:md5,28eafdfa41f98475e5e651fd0e8f95f2",
                 "cd4.peaks.txt:md5,4ab7c16a5f6d0e78275448bbce7c21c2",
                 "jurkat.bed:md5,7e59345b336cc8a9c5f96bf7df7b3d06",
diff --git a/workflows/tests/inputs/gff/main.nf.test.snap b/workflows/tests/inputs/gff/main.nf.test.snap
index d2564104..0ffc76f9 100644
--- a/workflows/tests/inputs/gff/main.nf.test.snap
+++ b/workflows/tests/inputs/gff/main.nf.test.snap
@@ -91,8 +91,6 @@
                 }
             },
             [
-                "bed2saf",
-                "bed2saf/cd4_intersect.saf",
                 "bwa",
                 "bwa/cd4_REP1.sorted.bam",
                 "bwa/cd4_REP1.sorted.bam.bai",
@@ -293,7 +291,6 @@
                 "transcript_identification/pints/jurkat_chr21_1_unidirectional_peaks.bed"
             ],
             [
-                "cd4_intersect.saf:md5,2528ed58898f6e1f9d3d54fc1381c4c6",
                 "cd4_REP1.sorted.bam.flagstat:md5,863e2d506d5cc4239af98a5f31bbc906",
                 "cd4_REP1.sorted.bam.idxstats:md5,b1dd8bcbd23c53c21f0e11082d9315f2",
                 "cd4_REP1.sorted.bam.stats:md5,1536c80bae78b2062508e1de210f6387",
@@ -323,8 +320,6 @@
                 "cd4_REP1.trimmed.fastp.json:md5,bd9a3344c1591d6be4d524451f9dca53",
                 "cd4_REP2.trimmed.fastp.json:md5,bc6e3f9ff7835f220535cc393b8eb25f",
                 "jurkat.trimmed.fastp.json:md5,65f7247a87479c7157c7357d575336e2",
-                "cd4_filtered.bed:md5,fe48a92889bc118c41e436989f85c65e",
-                "jurkat_filtered.bed:md5,f1dde43c4ad9dec972ff9fa38cc6f2fe",
                 "cd4.bed:md5,b55e5290d78941f36c3d1ecfef8e0062",
                 "cd4.peaks.txt:md5,bdcd2ec3a56a8a4a01ed19e17da003f2",
                 "jurkat.bed:md5,383cfaf10535dbe5d7f47607e345f4cb",
diff --git a/workflows/tests/inputs/gzipped_gff/main.nf.test.snap b/workflows/tests/inputs/gzipped_gff/main.nf.test.snap
index 290cc552..4660736c 100644
--- a/workflows/tests/inputs/gzipped_gff/main.nf.test.snap
+++ b/workflows/tests/inputs/gzipped_gff/main.nf.test.snap
@@ -91,8 +91,6 @@
                 }
             },
             [
-                "bed2saf",
-                "bed2saf/cd4_intersect.saf",
                 "bwa",
                 "bwa/cd4_REP1.sorted.bam",
                 "bwa/cd4_REP1.sorted.bam.bai",
@@ -293,7 +291,6 @@
                 "transcript_identification/pints/jurkat_chr21_1_unidirectional_peaks.bed"
             ],
             [
-                "cd4_intersect.saf:md5,2528ed58898f6e1f9d3d54fc1381c4c6",
                 "cd4_REP1.sorted.bam.flagstat:md5,863e2d506d5cc4239af98a5f31bbc906",
                 "cd4_REP1.sorted.bam.idxstats:md5,b1dd8bcbd23c53c21f0e11082d9315f2",
                 "cd4_REP1.sorted.bam.stats:md5,1536c80bae78b2062508e1de210f6387",
@@ -323,8 +320,6 @@
                 "cd4_REP1.trimmed.fastp.json:md5,bd9a3344c1591d6be4d524451f9dca53",
                 "cd4_REP2.trimmed.fastp.json:md5,bc6e3f9ff7835f220535cc393b8eb25f",
                 "jurkat.trimmed.fastp.json:md5,65f7247a87479c7157c7357d575336e2",
-                "cd4_filtered.bed:md5,fe48a92889bc118c41e436989f85c65e",
-                "jurkat_filtered.bed:md5,f1dde43c4ad9dec972ff9fa38cc6f2fe",
                 "cd4.bed:md5,b55e5290d78941f36c3d1ecfef8e0062",
                 "cd4.peaks.txt:md5,bdcd2ec3a56a8a4a01ed19e17da003f2",
                 "jurkat.bed:md5,383cfaf10535dbe5d7f47607e345f4cb",
diff --git a/workflows/tests/inputs/only_gff/main.nf.test.snap b/workflows/tests/inputs/only_gff/main.nf.test.snap
index 0b73cc6d..77e4d408 100644
--- a/workflows/tests/inputs/only_gff/main.nf.test.snap
+++ b/workflows/tests/inputs/only_gff/main.nf.test.snap
@@ -94,8 +94,6 @@
                 }
             },
             [
-                "bed2saf",
-                "bed2saf/cd4_intersect.saf",
                 "bwa",
                 "bwa/cd4_REP1.sorted.bam",
                 "bwa/cd4_REP1.sorted.bam.bai",
@@ -296,7 +294,6 @@
                 "transcript_identification/pints/jurkat_chr21_1_unidirectional_peaks.bed"
             ],
             [
-                "cd4_intersect.saf:md5,2528ed58898f6e1f9d3d54fc1381c4c6",
                 "cd4_REP1.sorted.bam.flagstat:md5,863e2d506d5cc4239af98a5f31bbc906",
                 "cd4_REP1.sorted.bam.idxstats:md5,b1dd8bcbd23c53c21f0e11082d9315f2",
                 "cd4_REP1.sorted.bam.stats:md5,1536c80bae78b2062508e1de210f6387",
@@ -326,8 +323,6 @@
                 "cd4_REP1.trimmed.fastp.json:md5,bd9a3344c1591d6be4d524451f9dca53",
                 "cd4_REP2.trimmed.fastp.json:md5,bc6e3f9ff7835f220535cc393b8eb25f",
                 "jurkat.trimmed.fastp.json:md5,65f7247a87479c7157c7357d575336e2",
-                "cd4_filtered.bed:md5,fe48a92889bc118c41e436989f85c65e",
-                "jurkat_filtered.bed:md5,f1dde43c4ad9dec972ff9fa38cc6f2fe",
                 "cd4.bed:md5,b55e5290d78941f36c3d1ecfef8e0062",
                 "cd4.peaks.txt:md5,bdcd2ec3a56a8a4a01ed19e17da003f2",
                 "jurkat.bed:md5,383cfaf10535dbe5d7f47607e345f4cb",
diff --git a/workflows/tests/transcript_indentification/grohmm/only_gff/main.nf.test.snap b/workflows/tests/transcript_indentification/grohmm/only_gff/main.nf.test.snap
index dfe1bafa..66d1544f 100644
--- a/workflows/tests/transcript_indentification/grohmm/only_gff/main.nf.test.snap
+++ b/workflows/tests/transcript_indentification/grohmm/only_gff/main.nf.test.snap
@@ -104,9 +104,6 @@
                 }
             },
             [
-                "bed2saf",
-                "bed2saf/cd4_intersect.saf",
-                "bed2saf/jurkat_intersect.saf",
                 "bwa",
                 "bwa/cd4_REP1.sorted.bam",
                 "bwa/cd4_REP1.sorted.bam.bai",
@@ -326,8 +323,6 @@
                 "transcript_identification/pints/jurkat_chr21_1_unidirectional_peaks.bed"
             ],
             [
-                "cd4_intersect.saf:md5,f1a0ef77b0e1409b859bba18190788ae",
-                "jurkat_intersect.saf:md5,8a0c5a2917d938c5bd055546eac53a99",
                 "cd4_REP1.sorted.bam.flagstat:md5,98ee509d07c1db03ccce634ccf410d07",
                 "cd4_REP1.sorted.bam.idxstats:md5,3f30696c4c8628b47029f63d9521f0e7",
                 "cd4_REP1.sorted.bam.stats:md5,4902e9a7e501f6150549e195b7dc44c0",
@@ -357,8 +352,6 @@
                 "cd4_REP1.trimmed.fastp.json:md5,bd9a3344c1591d6be4d524451f9dca53",
                 "cd4_REP2.trimmed.fastp.json:md5,bc6e3f9ff7835f220535cc393b8eb25f",
                 "jurkat.trimmed.fastp.json:md5,65f7247a87479c7157c7357d575336e2",
-                "cd4_filtered.bed:md5,e87e37f217df119d7b782150db375494",
-                "jurkat_filtered.bed:md5,e31353bc7016b44a2ad8a93dc26501e1",
                 "cd4.SE.tuning.csv:md5,9d76e9a83079d587459fda16af8c4da8",
                 "cd4.eval.txt:md5,de1f790f721a67dfd1e1bf1592a7971a",
                 "cd4.final.transcripts.bed:md5,3707df9ae8e7a95b6b5bfc336cfb1c8a",
diff --git a/workflows/tests/transcript_indentification/grohmm/tuning/main.nf.test.snap b/workflows/tests/transcript_indentification/grohmm/tuning/main.nf.test.snap
index 5f012660..093d9bbe 100644
--- a/workflows/tests/transcript_indentification/grohmm/tuning/main.nf.test.snap
+++ b/workflows/tests/transcript_indentification/grohmm/tuning/main.nf.test.snap
@@ -95,9 +95,6 @@
                 }
             },
             [
-                "bed2saf",
-                "bed2saf/cd4_intersect.saf",
-                "bed2saf/jurkat_intersect.saf",
                 "bwa",
                 "bwa/cd4_REP1.sorted.bam",
                 "bwa/cd4_REP1.sorted.bam.bai",
@@ -317,8 +314,6 @@
                 "transcript_identification/pints/jurkat_chr21_1_unidirectional_peaks.bed"
             ],
             [
-                "cd4_intersect.saf:md5,e2e38ad07e9363e5c71a72d2faeec6ca",
-                "jurkat_intersect.saf:md5,cd18a95027d48289248d33d70b863fa4",
                 "cd4_REP1.sorted.bam.flagstat:md5,863e2d506d5cc4239af98a5f31bbc906",
                 "cd4_REP1.sorted.bam.idxstats:md5,b1dd8bcbd23c53c21f0e11082d9315f2",
                 "cd4_REP1.sorted.bam.stats:md5,1536c80bae78b2062508e1de210f6387",
@@ -348,8 +343,6 @@
                 "cd4_REP1.trimmed.fastp.json:md5,bd9a3344c1591d6be4d524451f9dca53",
                 "cd4_REP2.trimmed.fastp.json:md5,bc6e3f9ff7835f220535cc393b8eb25f",
                 "jurkat.trimmed.fastp.json:md5,65f7247a87479c7157c7357d575336e2",
-                "cd4_filtered.bed:md5,2e235f9fe4e337a4e3f14c459ecd7988",
-                "jurkat_filtered.bed:md5,75086096f2ee6dab198228a0d2af1fad",
                 "cd4.SE.tuning.csv:md5,00e1c530e2ce3b09fd413b8f87eef5d0",
                 "cd4.eval.txt:md5,6f688621a2acb60f2e48163f132d390c",
                 "cd4.final.transcripts.bed:md5,5eb7209e5bb45744ae03f89010a162aa",