diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 0b753a453d..459b490e11 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -32,6 +32,7 @@ jobs:
             NXF_EDGE: "1"
         test:
           - "aligner"
+          - "alignment_to_fastq"
           - "annotation"
           - "cnvkit"
           - "controlfreec"
diff --git a/CHANGELOG.md b/CHANGELOG.md
index c9df2d2c11..5ea23e3fd2 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -103,6 +103,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#599](https://github.com/nf-core/sarek/pull/599) - Add checks for correct data type for `params.step`
 - [#599](https://github.com/nf-core/sarek/pull/599) - Add checks for no empty `--tools` with `--step variant_calling` or `--step annotation`
 - [#600](https://github.com/nf-core/sarek/pull/600) - Remove `nf-core lint` warnings
+- [#602](https://github.com/nf-core/sarek/pull/602/) - Fixed bug in `alignment_to_fastq` and added tests
 
 ### Deprecated
 
diff --git a/conf/test.config b/conf/test.config
index 3cc63737f9..e61e2e9945 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -26,7 +26,7 @@ params {
     max_time   = '8.h'
 
     // Input data
-    input = "${baseDir}/tests/csv/3.0/fastq_single.csv"
+    input = "${projectDir}/tests/csv/3.0/fastq_single.csv"
 
     // Small reference genome
     genome            = null
@@ -48,37 +48,37 @@ params {
 
 profiles {
     annotation {
-        params.input               = "${baseDir}/tests/csv/3.0/vcf_single.csv"
+        params.input               = "${projectDir}/tests/csv/3.0/vcf_single.csv"
         params.step                = 'annotate'
     }
     no_intervals {
         params.no_intervals        = true
     }
     pair {
-        params.input               = "${baseDir}/tests/csv/3.0/fastq_pair.csv"
+        params.input               = "${projectDir}/tests/csv/3.0/fastq_pair.csv"
     }
     markduplicates_bam {
-        params.input               = "${baseDir}/tests/csv/3.0/mapped_single_bam.csv"
+        params.input               = "${projectDir}/tests/csv/3.0/mapped_single_bam.csv"
         params.step                = 'markduplicates'
     }
     markduplicates_cram {
-        params.input               = "${baseDir}/tests/csv/3.0/mapped_single_cram.csv"
+        params.input               = "${projectDir}/tests/csv/3.0/mapped_single_cram.csv"
         params.step                = 'markduplicates'
     }
     prepare_recalibration_bam {
-        params.input               = "${baseDir}/tests/csv/3.0/mapped_single_bam.csv"
+        params.input               = "${projectDir}/tests/csv/3.0/mapped_single_bam.csv"
         params.step                = 'prepare_recalibration'
     }
     prepare_recalibration_cram {
-        params.input               = "${baseDir}/tests/csv/3.0/mapped_single_cram.csv"
+        params.input               = "${projectDir}/tests/csv/3.0/mapped_single_cram.csv"
         params.step                = 'prepare_recalibration'
     }
     recalibrate_bam {
-        params.input               = "${baseDir}/tests/csv/3.0/prepare_recalibration_single_bam.csv"
+        params.input               = "${projectDir}/tests/csv/3.0/prepare_recalibration_single_bam.csv"
         params.step                = 'recalibrate'
     }
     recalibrate_cram {
-        params.input               = "${baseDir}/tests/csv/3.0/prepare_recalibration_single_cram.csv"
+        params.input               = "${projectDir}/tests/csv/3.0/prepare_recalibration_single_cram.csv"
         params.step                = 'recalibrate'
     }
     save_bam_mapped {
@@ -100,7 +100,7 @@ profiles {
         params.nucleotides_per_second  = 20
     }
     tools {
-        params.input               = "${baseDir}/tests/csv/3.0/recalibrated.csv"
+        params.input               = "${projectDir}/tests/csv/3.0/recalibrated.csv"
         params.dbsnp               = params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz']
         params.fasta               = params.test_data['homo_sapiens']['genome']['genome_21_fasta']
         params.germline_resource   = params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz']
@@ -113,7 +113,7 @@ profiles {
         params.nucleotides_per_second = 20
     }
     tools_germline {
-        params.input               = "${baseDir}/tests/csv/3.0/recalibrated_germline.csv"
+        params.input               = "${projectDir}/tests/csv/3.0/recalibrated_germline.csv"
         params.dbsnp               = params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz']
         params.known_indels        = params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz']
         params.fasta               = params.test_data['homo_sapiens']['genome']['genome_21_fasta']
@@ -124,7 +124,7 @@ profiles {
         params.nucleotides_per_second = 20
     }
     tools_tumoronly {
-        params.input               = "${baseDir}/tests/csv/3.0/recalibrated_tumoronly.csv"
+        params.input               = "${projectDir}/tests/csv/3.0/recalibrated_tumoronly.csv"
         params.dbsnp               = params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz']
         params.fasta               = params.test_data['homo_sapiens']['genome']['genome_21_fasta']
         params.germline_resource   = params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz']
@@ -137,7 +137,7 @@ profiles {
         params.nucleotides_per_second = 20
     }
     tools_somatic {
-        params.input               = "${baseDir}/tests/csv/3.0/recalibrated_somatic.csv"
+        params.input               = "${projectDir}/tests/csv/3.0/recalibrated_somatic.csv"
         params.chr_dir             = params.test_data['homo_sapiens']['genome']['genome_21_chromosomes_dir']
         params.dbsnp               = params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz']
         params.fasta               = params.test_data['homo_sapiens']['genome']['genome_21_fasta']
@@ -158,14 +158,14 @@ profiles {
         params.trim_fastq          = true
     }
     umi {
-        params.input               = "${baseDir}/tests/csv/3.0/fastq_umi.csv"
+        params.input               = "${projectDir}/tests/csv/3.0/fastq_umi.csv"
         params.umi_read_structure  = '7M1S+T'
     }
     use_gatk_spark {
         params.use_gatk_spark      = 'baserecalibrator,markduplicates'
     }
     variantcalling_channels {
-        params.input               = "${baseDir}/tests/csv/3.0/recalibrated.csv"
+        params.input               = "${projectDir}/tests/csv/3.0/recalibrated.csv"
         params.fasta               = params.test_data['homo_sapiens']['genome']['genome_21_fasta']
         params.intervals           = params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed']
         params.wes                 = true
@@ -173,4 +173,7 @@ profiles {
 
         params.nucleotides_per_second = 20
     }
+    alignment_to_fastq {
+        params.input               = "${projectDir}/tests/csv/3.0/bam_for_remapping.csv"
+    }
 }
diff --git a/conf/test_full.config b/conf/test_full.config
index a32df0385b..cda0459c61 100644
--- a/conf/test_full.config
+++ b/conf/test_full.config
@@ -15,7 +15,7 @@ params {
     config_profile_description = 'Full test dataset to check pipeline function'
 
     // Input data for full size test
-    input = "${baseDir}/tests/csv/3.0/test_full_data.csv"
+    input = "${projectDir}/tests/csv/3.0/test_full_data.csv"
 
     wes   = true
 
diff --git a/subworkflows/nf-core/alignment_to_fastq.nf b/subworkflows/nf-core/alignment_to_fastq.nf
index 81720133d4..ec855d6ca2 100644
--- a/subworkflows/nf-core/alignment_to_fastq.nf
+++ b/subworkflows/nf-core/alignment_to_fastq.nf
@@ -50,17 +50,13 @@ workflow ALIGNMENT_TO_FASTQ {
 
     // join Mapped & unmapped fastq
     unmapped_reads = COLLATE_FASTQ_UNMAP.out.reads
-        .map{ meta, reads ->
-            fq_1 = reads.find{ it.toString().endsWith("_1.fq.gz") }
-            fq_2 = reads.find{ it.toString().endsWith("_2.fq.gz") }
-            [meta, [ fq_1, fq_2]]
+        .map{ meta, reads_R1_R2, reads_other, reads_singleton ->
+            [meta, reads_R1_R2]
         }
 
     mapped_reads = COLLATE_FASTQ_MAP.out.reads
-        .map{ meta, reads ->
-            fq_1 = reads.find{ it.toString().endsWith("_1.fq.gz") }
-            fq_2 = reads.find{ it.toString().endsWith("_2.fq.gz") }
-            [meta, [ fq_1, fq_2]]
+        .map{ meta, reads_R1_R2, reads_other, reads_singleton ->
+            [meta, reads_R1_R2]
         }
 
     reads_to_concat = mapped_reads.join(unmapped_reads)
diff --git a/tests/csv/3.0/bam_for_remapping.csv b/tests/csv/3.0/bam_for_remapping.csv
new file mode 100644
index 0000000000..9bc47d674f
--- /dev/null
+++ b/tests/csv/3.0/bam_for_remapping.csv
@@ -0,0 +1,2 @@
+patient,gender,status,sample,lane,bam,bai
+test,XX,0,test,1,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai
diff --git a/tests/test_bam_remap.yml b/tests/test_bam_remap.yml
new file mode 100644
index 0000000000..840c67b6e0
--- /dev/null
+++ b/tests/test_bam_remap.yml
@@ -0,0 +1,17 @@
+- name: Run alignment to fastq and then remap on bam files
+  command: nextflow run main.nf -profile test,alignment_to_fastq,docker -c ./tests/nextflow.config
+  tags:
+    - alignment_to_fastq
+
+  files:
+    - path: results/cat/test-1_1.merged.fastq.gz
+    - path: results/cat/test-1_2.merged.fastq.gz
+    - path: results/csv/markduplicates.csv
+    - path: results/csv/markduplicates_no_table.csv
+    - path: results/csv/recalibrated.csv
+    - path: results/multiqc/multiqc_report.html
+    - path: results/pipeline_info
+    - path: results/preprocessing/test
+    - path: results/reports
+    - path: results/samtools
+    - path: results/collate
diff --git a/workflows/sarek.nf b/workflows/sarek.nf
index f265f8eae5..05716260a9 100644
--- a/workflows/sarek.nf
+++ b/workflows/sarek.nf
@@ -1020,10 +1020,14 @@ def extract_csv(csv_file) {
 
         // start from BAM
         } else if (row.lane && row.bam) {
+            if (!row.bai) {
+                log.error "BAM index (bai) should be provided."
+            }
             meta.id         = "${row.sample}-${row.lane}".toString()
             def bam         = file(row.bam,   checkIfExists: true)
+            def bai         = file(row.bai,   checkIfExists: true)
             def CN          = params.seq_center ? "CN:${params.seq_center}\\t" : ''
-            def read_group  = "\"@RG\\tID:${row_sample}_${row.lane}\\t${CN}PU:${row.lane}\\tSM:${row.sample}\\tLB:${row.sample}\\tPL:${params.seq_platform}\""
+            def read_group  = "\"@RG\\tID:${row.sample}_${row.lane}\\t${CN}PU:${row.lane}\\tSM:${row.sample}\\tLB:${row.sample}\\tPL:${params.seq_platform}\""
 
             meta.numLanes   = numLanes.toInteger()
             meta.read_group = read_group.toString()
@@ -1031,7 +1035,7 @@ def extract_csv(csv_file) {
 
             meta.size       = 1 // default number of splitted fastq
 
-            if (params.step == 'mapping') return [meta, bam]
+            if (params.step == 'mapping') return [meta, bam, bai]
             else {
                 log.error "Samplesheet contains ubam files but step is `$params.step`. Please check your samplesheet or adjust the step parameter.\nhttps://nf-co.re/sarek/usage#input-samplesheet-configurations"
                 System.exit(1)